[Ifeffit] a Windows GUI for wavelet transformation of EXAFS
Dear XAS community, I would like to share a Windows GUI for wavelet transformation of EXAFS. It is written in Python by my student Zhihang Ye. There are also other applications developed by different groups. This one may be more user-friendly. The GUI, instructions, code, references, and other related information are in GITHUB. https://github.com/Himmelspol/wtEXAFS If you find any problems or have any suggestions, please let us know. -- Best Regards, Peng Liu School of Environmental Studies China University of Geosciences, Wuhan, Hubei Province, PR China https://scholar.google.com/citations?user=qUtyvokJ=en http://grzy.cug.edu.cn/049121/zh_CN/index.htm ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] S02 selection from reviewer
Dear IFEFFIT members, Thanks for all your suggestions, we got the idea to revise our manuscript without just comparing the CNs. We are also planning to provide more discussion for the selection of S02 and factors thay may affect it. Thanks for your in depth discussion. On Sun, Oct 3, 2021 at 12:08 PM John J Rehr wrote: > > Hi everyone > > I wonder how much effect on the expt value of S02 comes from background > subtraction including previous edges, the energy dependence of the atomic > background, and the range of the EXAFS. Theoretically S02 is nut a constant > but a spectral average. I’d like to see a careful study with a well defined > algorithm that could be compared with theoretical estimates. Thanks. > > John > > On Sat, Oct 2, 2021 at 8:47 AM Anatoly Frenkel < > anatoly.fren...@stonybrook.edu> wrote: > >> I think that the variability of S02 between different samples, detection >> methods etc. may or may not be a big concern for you if 1) the error bars >> in the CNs (that you are not reporting) are larger than the difference in >> their mean values (that you are reporting), and/or 2) larger than the >> difference between their mean values and the CN=6 that the reviewer is >> asking about. If yes to either 1) or 2), then the variability in the S02 >> values for differently prepared samples may cause smaller variation in your >> best fit values of CN than the error bars reported by your fitting program, >> and your choice of fixing your S02 to be constant (0.85) may be justified. >> You need to have a really bad non-uniformity or concentration problem so >> that your effective S02 changed from the expected 0.85 (assuming it is what >> a correctly performed measurement would give) to, say, 0.5 or 0.6 is my >> thought. >> >> >> Anatoly >> >> >> >> On Sat, Oct 2, 2021 at 3:50 AM Peng Liu wrote: >> >>> Dear IFEFFIT members, >>> >>> I am sorry to bother you again. I asked about S02 selection for the >>> first major revision. I just received the second revision. The reviewer is >>> not satisfied with one S02 value for all our samples. >>> " >>> >>> 1. I am still not satisfied with selected SO2 value (it is set to 0.85). >>> SO2 is not transferable between different samples and detection methods. It >>> is not possible to use a value obtained from different compound using >>> transmission measurement mode to completely different other compound >>> measured using fluorescence mode. One method to fix SO2 value is to measure >>> diluted solution (to avoid self-absorption) of reference material in >>> fluorescence mode. Other is to use multiple spectra fitting for all samples >>> of interest (e.g. with Sb(V)) measured using fluorescence mode where SO2 >>> parameter is the same for all samples. >>> >>> At the same time I am confident that CN values 5.6, 7.1 and 6.9 >>> correspond to CN(Sb-O)=6. I suggest reconsidering the SO2 value for >>> measurements in fluorescence mode. >>> " >>> >>> We do get the S02 from a similar reference material measured in >>> transmission mode, and our samples were all measured in fluorescence mode. >>> It is not possible to measure the diluted reference material in >>> fluorescence mode in one or two months. If you could give me some >>> suggestions, that would be great. >>> >>> >>> -- >>> Best Regards, >>> >>> Peng Liu >>> ___ >>> Ifeffit mailing list >>> Ifeffit@millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >>> >> ___ >> Ifeffit mailing list >> Ifeffit@millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >> > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > -- Best Regards, Peng Liu ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
[Ifeffit] S02 selection from reviewer
Dear IFEFFIT members, I am sorry to bother you again. I asked about S02 selection for the first major revision. I just received the second revision. The reviewer is not satisfied with one S02 value for all our samples. " 1. I am still not satisfied with selected SO2 value (it is set to 0.85). SO2 is not transferable between different samples and detection methods. It is not possible to use a value obtained from different compound using transmission measurement mode to completely different other compound measured using fluorescence mode. One method to fix SO2 value is to measure diluted solution (to avoid self-absorption) of reference material in fluorescence mode. Other is to use multiple spectra fitting for all samples of interest (e.g. with Sb(V)) measured using fluorescence mode where SO2 parameter is the same for all samples. At the same time I am confident that CN values 5.6, 7.1 and 6.9 correspond to CN(Sb-O)=6. I suggest reconsidering the SO2 value for measurements in fluorescence mode. " We do get the S02 from a similar reference material measured in transmission mode, and our samples were all measured in fluorescence mode. It is not possible to measure the diluted reference material in fluorescence mode in one or two months. If you could give me some suggestions, that would be great. -- Best Regards, Peng Liu ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] EXAFS Fitting with 2 CIF files
Just a quick question. For Zihao' sample, the 1st peak for Pt-O from PtO2 is at 2.07 A and the 2nd peak for Pt-Pt or Pt-Fe from Pt3-Fe is at 2.736 A. If these peaks are at different positions, could we use the molar ratio method to distinguish the contribution from each reference? My understanding is that if two paths contribute to the same peak, then the molar ratio method can be applied. I am not sure if my understanding is right or not. Best Regards, Peng Liu China University of Geosciences On Sun, Sep 5, 2021 at 5:00 AM Matthew Marcus wrote: > Extending what Scott said, I find it useful to make the coefficients > abs(fracoxide) and abs(1-abs(fracoxide)) to avoid false minima with > negative S0^2. > mam > > On 9/4/2021 1:21 PM, Scott Calvin wrote: > > Hi Zihao, > > > > Do it by folding the molar ratio in to the amp parameter for each CIF. > Of course S02 is part of that parameter, too. > > > > So the amp for PtO2 might be parameterized as S02 * fracoxide and the > amp for Pt3Fe as S02 * (1-fracoxide) > > > > You could either assume the S02 is the same for the two phases (as I > implicitly did by writing it with only one S02 variable), or you could use > a standard for each (from a sample prepared and measured in a similar way) > to fix the S02 for each phase. > > > > Best, > > Scott Calvin > > Lehman College of the City University of New York > > > >> On Sep 4, 2021, at 4:02 PM, Zihao Yan wrote: > >> > >> Dear Ifeffit members: > >> > >> I have a sample which is a mixture of PtFe and PtO2. In order to do the > EXAFS fitting, I imported 2 CIF files on Artemis and generated the > following 3 paths: > >> From PtO2: Pt-O @ 2.07 nm > >> From Pt3Fe: Pt-Pt @ 2.736 nm, Pt-Fe @ 2.736 nm > >> Then, I used these 3 bonds to do the fitting as in the online tutorial > (which used 1 CIF file). The fitting result is good in terms of R^2 but it > is not scientifically correct. > >> > >> I think I didn't set up a parameter which determines the ratio between > CIF(PtO2) and CIF(Pt3Fe). I mean there should be a parameter that regulates > how much each CIF contributes to the fitting or the molar ratio between > PtO2 and Pt3Fe in my system. > >> > >> Could someone please give me some suggestions on how to do EXAFS > fitting with 2 CIF files? Is there anywhere I can set up the molar ratio > between PtO2 and Pt3Fe? > >> > >> Yours sincerely, > >> Zihao Yan > >> ___ > >> Ifeffit mailing list > >> Ifeffit@millenia.cars.aps.anl.gov > >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > > > > ___ > > Ifeffit mailing list > > Ifeffit@millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > -- Best Regards, Peng Liu ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
[Ifeffit] Manuscript comments regarding EXAFS modeling
Dear Ifeffit members, I received the following two comments. " Comment 1: Authors have fixed the amplitude reduction factor (SO2) to a fixed value (0.85). This factor is specific to particular chemical compound and sample preparation and quality (mostly homogeneity), measurement method (e.g. absorption, fluorescence). Authors can find in literature [e.g. Rehr2000] that SO2 for ideal samples (having no other effects) represent multielectron effects, which by definition depend on valence and ligands. Even more, SO2 is correlated with Debye-Waller factor (σ²) and coordination number (CN), so any chosen value will be compensated by CN and σ². As coordination numbers are used as quantitative indicators in discussion and following conclusions. I would request to clarify the selection criteria for SO2 values and advise to revise this approach (i.e. not to fix SO2 as the same value for all samples). I do not expect drastic changes in obtained CN values, but this should be tested. Comment 2: As I mentioned previously, coordination number (CN) is correlated with Debye-Waller factor (σ²). My question is: how this correlation is managed (eliminated)? Most probably (in FEFFIT) this is done by using 3 separate values for n (1,2,3), where n is a power in expression chi(k)*(k^n). " I used Artemis for the calculation. 1) Because S02 and CN are multiplication relations in the EXAFS equation, as we usually do, we fixed S02 to obtain CN for unknown samples. 2) there are outputs regarding the correlation between different fitting parameters from Artemis. Is there a way to manage or eliminate the correlation as the reviewer mentioned using Artemis or Larch? If you also could give me some suggestions to answer the comments, that would also be greatly appreciated. -- Best Regards, Peng Liu School of Environmental Studies China University of Geosciences, Wuhan, Hubei Province, PR China https://scholar.google.com/citations?user=qUtyvokJ=en http://grzy.cug.edu.cn/049121/zh_CN/index.htm ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
[Ifeffit] Undo in Athena
Hello everyone, I have one more question about undo in Athena, e.g. I accidentally deleted one of the good spectra, how I can get it back. In word, I can go to Edit and click undo, but I haven't found it in Athena. Thanks for your time, Peng -- Ph.D. Candidate Earth and Environmental Sciences, CEIT Bldg. Rm. 2026 University of WaterlooPh: 519-888-4567 ext. 37232 200 University Avenue West Waterloo, Ontario N2L 3G1Fax:519-746-3882 p26...@uwaterloo.ca ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] Import XAFS Data from Farrel Lytle Database (http://ixs.iit.edu/database/)
Hi all, I searched the Farel Lytle Database and looked like I found chalcopyrite spectra for Cu from http://ixs.iit.edu/database/data/Farrel_Lytle_data/RAW/Cu/index.html. I downloaded the data, but I can not import into Athena. I looked into the data, it looked wired for me. The first column doesn't look like energy for Cu. I am wondering if anyone have any idea how to import or transfer the data. I attached the data file. Regards, Peng -- Ph.D. Candidate Earth and Environmental Sciences, CEIT Bldg. Rm. 2026 University of WaterlooPh: 519-888-4567 ext. 37232 200 University Avenue West Waterloo, Ontario N2L 3G1Fax:519-746-3882 p26...@uwaterloo.ca NPTS NS CUEDGE CUHITE DSPACE STPDEG STEPMM STARTSTOP SCALE 468 3 84294. 20. 1.92017 4000. 3150. 85290. 75506.2.000 DELTA: 50. 5. 22. 36. 48. DELEND: 84788. 83804. 81216. 76752. 71076. SEC: 2.000 2.000 2.000 2.000 2.000 OFFSET: 1140. 1608. 401.4.4.6. 137.4.6. 18. 641. 3.2.5. 61. 20. 93. 232.0.0.0.0.0.0. SINGLE XTAL CUINSE2 CHALCOPYRITE 7 7 5-30-83 85290. 2.62740E+05 2.69329E+05 1.37453E+04 85240. 2.63329E+05 2.69903E+05 1.32863E+04 85190. 2.62699E+05 2.69422E+05 1.31963E+04 85140. 2.61994E+05 2.68895E+05 1.31268E+04 85090. 2.61453E+05 2.68538E+05 1.30418E+04 85040. 2.60785E+05 2.68062E+05 1.29858E+04 84990. 2.60028E+05 2.67461E+05 1.28778E+04 84940. 2.59236E+05 2.66832E+05 1.28148E+04 84890. 2.58560E+05 2.66316E+05 1.27378E+04 84840. 2.57993E+05 2.65934E+05 1.26993E+04 84790. 2.57192E+05 2.65293E+05 1.27238E+04 84740. 2.56507E+05 2.64779E+05 1.26123E+04 84735. 2.56674E+05 2.65012E+05 1.27078E+04 84730. 2.56887E+05 2.65249E+05 1.27523E+04 84725. 2.56154E+05 2.64440E+05 1.26368E+04 84720. 2.56329E+05 2.64673E+05 1.26843E+04 84715. 2.56113E+05 2.6E+05 1.27128E+04 84710. 2.56446E+05 2.64826E+05 1.27273E+04 84705. 2.55947E+05 2.64302E+05 1.27208E+04 84700. 2.56291E+05 2.64673E+05 1.27248E+04 84695. 2.55780E+05 2.64124E+05 1.26613E+04 84690. 2.55990E+05 2.64383E+05 1.27108E+04 84685. 2.55605E+05 2.63968E+05 1.26723E+04 84680. 2.55894E+05 2.64312E+05 1.27218E+04 84675. 2.55058E+05 2.63409E+05 1.25503E+04 84670. 2.55303E+05 2.63702E+05 1.26383E+04 84665. 2.55216E+05 2.63629E+05 1.26903E+04 84660. 2.55511E+05 2.63924E+05 1.27068E+04 84655. 2.55611E+05 2.64066E+05 1.27208E+04 84650. 2.55898E+05 2.64388E+05 1.28578E+04 84645. 2.55825E+05 2.64331E+05 1.28178E+04 84640. 2.55234E+05 2.63691E+05 1.27803E+04 84635. 2.55268E+05 2.63751E+05 1.27593E+04 84630. 2.54961E+05 2.63442E+05 1.27658E+04 84625. 2.55098E+05 2.63587E+05 1.27638E+04 84620. 2.54470E+05 2.62934E+05 1.27748E+04 84615. 2.54588E+05 2.63084E+05 1.27443E+04 84610. 2.53954E+05 2.62417E+05 1.26758E+04 84605. 2.54124E+05 2.62623E+05 1.26988E+04 84600. 2.53850E+05 2.62341E+05 1.26843E+04 84595. 2.53891E+05 2.62446E+05 1.27378E+04 84590. 2.54576E+05 2.63216E+05 1.29453E+04 84585. 2.54663E+05 2.63329E+05 1.29638E+04 84580. 2.54231E+05 2.62850E+05 1.28738E+04 84575. 2.54398E+05 2.63065E+05 1.29358E+04 84570. 2.54572E+05 2.63252E+05 1.30038E+04 84565. 2.54527E+05 2.63225E+05 1.30218E+04 84560. 2.54183E+05 2.62889E+05 1.30558E+04 84555. 2.54387E+05 2.63124E+05 1.30938E+04 84550. 2.53632E+05 2.62309E+05 1.29698E+04 84545. 2.53779E+05 2.62504E+05 1.30058E+04 84540. 2.53711E+05 2.62423E+05 1.30578E+04 84535. 2.53806E+05 2.62573E+05 1.30878E+04 84530. 2.53443E+05 2.62177E+05 1.31223E+04 84525. 2.53673E+05 2.62465E+05 1.31653E+04 84520. 2.53002E+05 2.61739E+05 1.30518E+04 84515. 2.53242E+05 2.62024E+05 1.30948E+04 84510. 2.52940E+05 2.61718E+05 1.31593E+04 84505. 2.53206E+05 2.62026E+05 1.32078E+04 84500. 2.54107E+05 2.63049E+05 1.34943E+04 84495. 2.54317E+05 2.63286E+05 1.35813E+04 84490. 2.52789E+05 2.61595E+05 1.32793E+04 84485. 2.52997E+05 2.61858E+05 1.33278E+04 84480. 2.50979E+05 2.59652E+05 1.29903E+04 84475. 2.51198E+05 2.59921E+05 1.30453E+04 84470. 2.51339E+05 2.60108E+05 1.32198E+04 84465. 2.51797E+05 2.60612E+05 1.32753E+04 84460. 2.51716E+05 2.60529E+05 1.34003E+04 84455. 2.51748E+05 2.60576E+05 1.34403E+04 84450. 2.52445E+05 2.61346E+05 1.36928E+04 84445. 2.52573E+05 2.61517E+05 1.37278E+04 84440. 2.51574E+05 2.60421E+05 1.36693E+04 84435. 2.51689E+05 2.60599E+05 1.36873E+04 84430. 2.51963E+05 2.60922E+05 1.38693E+04 84425. 2.52106E+05 2.61099E+05 1.39708E+04 84420. 2.50991E+05 2.59896E+05 1.39283E+04 84415. 2.51205E+05 2.60151E+05 1.39608E+04 84410. 2.51709E+05 2.60726E+05 1.41528E+04 84405. 2.51660E+05 2.60700E+05 1.42468E+04 84400. 2.51470E+05 2.60489E+05 1.43853E+04 84395. 2.51864E+05
