Re: [Ifeffit] S02 and k_min

2012-12-02 Thread Anatoly I Frenkel
ello everyone, I am currently performing a simple curve fit on bulk MoS2 using an atoms file for crystalline MoS2. I've found that increasing k_min on my fit (e.g. from 2 to 4) improves the quality of the fit (R-factor from 0.028 to 0.009), but also increases S02. If I use a large enough k_mi

[Ifeffit] phase problem copper

2015-07-14 Thread Neeb, Matthias
Dear all, I have a standard exafs spectrum of copper K-shell and everything looks as expected (Chi(E), Chi(k), Chi(R), Chi(q) …) when using Demeter 0.9.21 . However the phase spectrum of (Chi(q)) appears quite different to literature (e.g. B.K. Teo, Inorganic Chemistry Concepts 9; Martens et

[Ifeffit] Fitting Problems in Artemis version 0.9.26

2018-06-28 Thread LIU HUAN
s 0.9). (2) When Fitting the Debye�CWaller factor (ss) and coordination number (N), although I use "abs()" to make it to be positive, but the fitting results still be negative. But I did not meet these problems in the old version in Artemis 0.8.012. I am wondering that whether coul

Re: [Ifeffit] Asymmetric error bars in IFeffit

2010-10-24 Thread Scott Calvin
I don't think it's at all strange, Anatoly, and I think Matthew's solution is the right one--it seems obvious in retrospect that the parameter that Ifeffit should evaluate is 1/R, but apparently it wasn't obvious to me on Friday. :) As for obtaining N instead of R, t

Re: [Ifeffit] Consistency criterion

2006-09-28 Thread Juan Antonio Maciá Agulló
Hi Scott, Thanks a lot, you are a good fortune-teller. I have low-Z scatterers (oxygen) and high-Z scatteres (Pt). Best regards, JA Scott Calvin ha escrito: > Hi Juan, > > They're consistent. The higher r-factor on the kwt-1 data might be a > clue about how reliable part o

Re: [Ifeffit] Multiple data set fit limit

2017-03-10 Thread Bruce Ravel
On 03/09/2017 05:15 AM, Victor Streltsov wrote: 3 data set refined to completion with sensible refined parameter, however, R-factor for 3^rd data set is 1. (overall R for 3 data set is huge too) and after-fit plot for 3^rd data set is missing, only experimental one shown. I am using latest

Re: [Ifeffit] problem of overestimated E0 (Edge-energy)

2012-01-13 Thread JeongEunSuk
=11563eV, Rbkg=1.3, kweight =1 To fit data k -range = 3.0~13.5, R -range =2.3~13.5 1. fitting parameters set macc = 0.0 set so2 = 0.89// reduction factor guess ePt = 0.0 // energy shift set npt1=1.0// the number of Pt (1.0 means 12&nb! sp; Pt a

Re: [Ifeffit] Question on (Combo-) LCF plot output

2020-03-30 Thread Peloquin, Derek
bles, and approximately 41.333 measurements Weights sum to 1: no Weights forced between 0 and 1: no Overall e0 shift used: yes Noise added to data: 0 R-factor = 0.0003537 Chi-square = 0.00815 Reduced chi-square = 0.858 .standard weight e0

Re: [Ifeffit] Estimation of S02

2008-10-08 Thread Hiroshi Oji
Hi Matthias and Leandro, Thank you very much for your reply. I checked the DW-factor (MSRD) and found it also varies significantly depending on Fit k-weight as follows. kw amp ss 1 0.8145660 +/- 0.0486470 0.0073230 +/- 0.0005240 2 0.9230700 +/- 0.0673820

Re: [Ifeffit] Data being overwritten in Artemis history window

2015-03-10 Thread Bruce Ravel
previous fit it will have been overwritten by the newer fit. Some of the other info, such as R-factor by k-weight seems to get overwritten too. I just pushed a fix for this to github and posted new windows installer candidates at http://bruceravel.github.io/demeter/#windows If you see any oth

Re: [Ifeffit] Fitting XANES spectrun with standards (Adrien Couet)

2012-06-29 Thread Bruce Ravel
el file > attached). > In the case of the single fit I get a R-factor of 2.0x10-3 whereas for the > best fit from the combinations I got 1.8x10-3 (the weights of each > standards are also different in both cases). My answer is still the same. It is quite possible that I am not unders

[Ifeffit] Problems with EXAFS Fitting of Metalloprotein Zinc Samples

2015-11-10 Thread Carolyn Carr
likes it. 5 imidazoles and 3 sulfurs and I have an R-factor of 0.2% every time. If there is non standard multiple scattering that occurs in multiple unrelated proteins from different organisms then we would have no idea what this could be. Thanks for your comments! Carolyn Carr

Re: [Ifeffit] Large Amplitude Values

2010-07-31 Thread Scott Calvin
Hi Gavin, What are the uncertainties on the high S02 values? Fluorescence is unlikely to be the culprit. While it can affect your ability to normalize properly, you're unlikely to account for a factor of 2 by normalization if the data is relatively decent. And self- absorption ten

Re: [Ifeffit] Athena crash during LCA

2011-01-07 Thread Jeff Terry
Hi Scott, No my fault, I suffer from tl;dr itis. I didn't read beyond linear combination. That said it still works: Fitting Data as chi(k) from 3.000 to 12.000 fit done use k-weight = 2 Fit included 181 data points and 1 variable R-factor = 0.209356 chi-square = 30.92638 reduce

Re: [Ifeffit] Questions about Athena and XANES

2008-02-21 Thread Jeff Terry
there is a photoelectron spectrum showing the relative intensity of Auger and Photopeaks. The secondaries are roughly a factor of 100 more intense than the other contributions. It is possible to measure both TEY and Auger electron yield (AEY) and you will see that the AEY is more surface sensitiv

Re: [Ifeffit] amplitude parameter S02 larger than 1

2015-03-20 Thread Scott Calvin
Hi Yanyun, Good. So here's the procedure for a Hamilton test. We're comparing the fit with S02 guessed to the one with S02 set to 0.90, because that was your a priori best guess at S02. I take the ratio of the first R-factor to the second. You didn't actually say the R-factor f

Re: [Ifeffit] weighting multi-data fit

2007-06-19 Thread Matt Newville
one. For fits in R space, epsilon_r is used as the weighting factor: For a single data set, the quantity minimized in the best fit is chi_square = (1 / N ) Sum_i=1^N { [Data_i - Fit_i]^2 / epsilon_r^2 } where the sum is over N R-space points. The data spacing for chi(R) is set by the Fo

Re: [Ifeffit] Inversion Degree

2019-07-06 Thread Juan de la figuera
ed to firstly obtain the (short-ranged) lattice parameter > (in angstrom) of each phase from an EXAFS fitting with an R-factor less > than 0.02. > Then the volume (in angstrom cube) of the unit cell of each phase is > known. Given that the number of Co atoms /unit cell is known for each >

Re: [Ifeffit] LCF analysis

2010-10-25 Thread Scott Calvin
very, very noisy data. Including C in the fit might very well improve the fit in the sense of an R-factor--maybe, in fact, there's a 45% chance of a modest improvement with a given set of very noisy data, even if there's no C present. That does not mean that a result like tha

Re: [Ifeffit] S02 and k_min

2012-12-02 Thread Matt Newville
Hi Mike, On Sun, Dec 2, 2012 at 11:54 AM, Michael Morrill wrote: > Hello everyone, > > I am currently performing a simple curve fit on bulk MoS2 using an atoms file > for crystalline MoS2. I've found that increasing k_min on my fit (e.g. from 2 > to 4) improves the quality

Re: [Ifeffit] Energy Resolution

2018-05-10 Thread Carlo Segre
measurement you are making (transmission, fluorescence). All of these factors can masquerade a amplitude reduction factor. What I do in practice is to measure a standard which has the same local environment and fit the EXAFS with the known structure to extract an S02 which I then use

Re: [Ifeffit] Question about PCA

2019-04-24 Thread Matt Newville
Hi Joselaine, On Wed, Apr 24, 2019 at 8:40 PM Joselaine Cáceres gonzalez < joselainecace...@gmail.com> wrote: > Hi Matt, thank you for your answer!. The references I have about > Malinowski´s work and some applications are: > > Malinowski, E.R., *Theory of error in factor ana

[Ifeffit] Use of the 3rd and 4th Parameter

2014-06-16 Thread Michael Kömm
actly 0.0 with no fit taking place (enot = 0, amp = 0 (guess amp = 1) delr = 0 and ss = 0.003) and the R-factor of the fit is way over the top (>10^20). I've chosen a value of 0.5 for the 3rd and the 4th parameter just to see if they're working and I was only doing a quick first

[Ifeffit] Consistency criterion

2006-09-28 Thread Juan Antonio Maciá Agulló
Hi all, Scott answered my question about consistency but now I have a new doubt. I have two fits (one in k1 and other in k3 weights) with fitted parameters that have uncertainty ranges overlaped, then... in principle, they are consitent, right? But the fit in k1 weight have a R-factor too high

[Ifeffit] Yttrium in alumina GBs

2006-12-20 Thread Shantanu Behera
to 0.005, my CN jumps from 4.8 to 5.2. When I make a cluster based on Yttria structure, I get DW factor of 0.008 +- 0.002, unrestrained. While I restrain the DW to 0.01, it again jumps from 4.8 to 5.2. First query...if you can pin down on the CN change (Carlo..you wanted some numbers) Second

[Ifeffit] Exafs distance resolution

2007-11-27 Thread Eric Breynaert
Dear all, Is there a physical limitation determining exafs bond distance resolution? Very often the equation r = pi / 2 deltak is quoted as a measure for bond distance resolution. But as i understand this equation is related to the fourier transform traditionally used for exafs analysis. If

[Ifeffit] Linear Combination Fitting - More Questions

2008-07-17 Thread Gudrun Lisa Bovenkamp
myself and someone can correct me: Certainly not all of my, say 10 reference spektra, are that similar that I can get several LCFs with the same say R-factor. So, I will get some clue to narrow the components. But still there can be, for example: Standard-combi 1, 2, 3 equal to 1, 4, 6. So, my

Re: [Ifeffit] Cadmium K-edge

2011-01-11 Thread Alan Du
(CdTiO3). No multiple >> scattering paths used. The best fit goes something like this: >> >> >> ******** >> Independent points = 13.166992187 >> Number of variables = 8.

Re: [Ifeffit] Estimation of S02

2008-10-09 Thread Hiroshi Oji
you were hoping for. > > Regarding your Athena project, I suggest tweaking the position of E0 > and the k and R windows according to the advice provided in the links > above. The experimental data looks nice and clean up to k~14.5 A-1. > > Best of luck, > Leandro > &

Re: [Ifeffit] amplitude parameter S02 larger than 1

2015-03-23 Thread Matt Newville
means that the estimated > uncertainties really aren't dependable for fits that are known to be bad > (e.g. have a huge R-factor, unrealistic fitted parameters, etc.), but since > those fits aren't generally the published ones, that's OK. > > Secondly, the high-

Re: [Ifeffit] Transferabillity of So2

2009-03-23 Thread Iztok Arčon
Dear Scott, There are several papers dealing with effects of multielectron photoexcitations present in atomic absorption background (AAB) of K and L edge EXAFS spectra, which are responsible for the amplitude reduction factor S02. A quantitative analysis of shake-up, shake-off and other

Re: [Ifeffit] About export Chi(K) file

2010-02-04 Thread Bruce Ravel
d it seemed > a good fitting from the figure in Graphic window #1 - [Athena]. But the > results showed that only path 1 had good values of N, R-factor, > Chi-square, amp and sigma^2. If I choose only path 1 for fitting, the > figure in Graphic window #1 - [Athena] showed only the highest

Re: [Ifeffit] Hephaestus: Absorption Data Source

2017-11-13 Thread Robert Gordon
misleading. Lifetimes derived from theory and experiment often differ by a factor of 2 or more. In the transition metals of the first period plots of measured widths of the L1(2s),L2(2p12), and L3(2p32) levels as a function of atomic number show broad maxima which are not adequately described by theory

Re: [Ifeffit] Issue with the Athena software - Athena Warning: redundant argument in sprintf

2019-10-15 Thread Ravel, Bruce
utside its error bar. Also, the R factor for fit "B,D,E" is barely different from those above, which further suggests that those two are not actually in your sample. What happens if you exclude those two from the combinatorial fit? Do you see the same error message? What happen

Re: [Ifeffit] Estimation of S02

2008-10-08 Thread Matthias Bauer
hi hiroshi, i did not have a look at the attached project, but what paramteres did you vary? even if you use different k-weightings, there is still the strong correlation of N,S02 and the Debye-Waller like factor. so as long as you do not keep two of these three on a certain value, your S02 might

Re: [Ifeffit] Using windows apj files on linux

2007-05-30 Thread Ravel, Bruce D.
er of variables : 0 Chi-square : 0 Reduced chi-square : 0 R-factor : 0 Measurement uncertainty (k) : 0 Measurement unc

Re: [Ifeffit] weighting multi-data fit

2007-06-20 Thread Jörg Haug
_k for each data set. > The two values are related and specifying either one is sufficient for > the feffit() command to calculate the appropriate one. For fits in R > space, epsilon_r is used as the weighting factor: For a single data > set, the quantity minimized in the best fit is

Re: [Ifeffit] Analyzing EXAFS data on Artemis

2021-05-27 Thread Matt Newville
t higher k than normal (perhaps 4 or 5 Ang^-1) or increasing the k-weight used in the Fourier transform (perhaps to 3 or 4) would de-emphasize the Se-Li scattering to a level that it was safe(r) to ignore. FWIW, I would imagine that trying to fit coordination number or sigma^2 for Se-Li at per

Re: [Ifeffit] Demeter 0.9.26 launch faillure

2017-12-06 Thread Robert Gordon
er-supplied value of epsilon_k for fitting multiple dataset. If it is difficult to make the version 0.9.26 available soon, maybe in 0.9.25 there is a possibility to set R-factor as a figure of merit for fitting rather than chi^2? That might also help. Thank you All the best, Kirill Lomachenk

Re: [Ifeffit] Problems with EXAFS Fitting of Metalloprotein Zinc Samples

2015-11-09 Thread Robert Gordon
minima. For Cobalt and Nickel samples I typically get one or a few fits that are obviously significantly better in R-factor (with reasonable distances, sigma^2, etc) but for Zinc this is not the case. I can get many good fits and Zinc likes to increase the coordination up to 8 for all data sets I

Re: [Ifeffit] Artemis fit error - chi-square and R-factors are always equal to 0

2021-03-26 Thread Matt Newville
Hi Ava, Sorry for the trouble. It looks to me like the fit actually ran. Like, getting non-trivial and non-starting values and uncertainties for 'ss_Cu1', 'dr_Cu1', etc tells me that many parts of the fit and code worked. I'm not at all sure why Chi-square and R-f

Re: [Ifeffit] LCF analysis

2010-10-25 Thread Wayne W Lukens Jr
in the data, the > fit would indicate that C was present when it was not. That is *not* the > same thing as saying there is a 77% chance of C being present. > > To see this, imagine very, very noisy data. Including C in the fit might > very well improve the fit in the sense of an R-factor

Re: [Ifeffit] Unwanted rescaling of energy axis when importing ascii file into Athena (Demeter 0.9.26)

2019-01-09 Thread Ravel, Bruce
ilar to the one reported in March 2018 under the > topic "Athena (Demeter 0.9.26) does not import all datapoints from ascci > file". However, the issue I am seeing always results in 1.2eV steps in > the imported data. If my original file hast 0.3eV steps, the number of > po

Re: [Ifeffit] Question about transform windows and statistical parameters

2011-05-13 Thread Scott Calvin
679339    10.5     0.090364699   11        0.092509939      11.5     0.108103081    There's a general trend of increasing epsilon_r with an increase in k. There's also a jump of a factor of 2 between 7.5 and 8. Why? Because there's a glitch there, and the glitch adds high-R structure.To make sur

Re: [Ifeffit] problem with E0 (enot) parameters

2009-06-22 Thread Zajac, Dariusz A.
parameters" # - # fitFoM R-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.

Re: [Ifeffit] Energy Resolution

2018-05-10 Thread Lorenzo Stievano
measurement you are making (transmission, fluorescence).  All of these factors can masquerade a amplitude reduction factor. What I do in practice is to measure a standard which has the same local environment and fit the EXAFS with the known structure to extract an

[Ifeffit] Athena (linear combination fitting)

2011-05-12 Thread Dilnesa, Belay
diffcult because the R factor of the first 5 combinations with diffrent reference combinations is similar. And as I see from my fitting the alignement plays really an important role on the LCF. You know when I made allign marked groups based on the standard, it alligns well the enregy but when I

Re: [Ifeffit] Exafs distance resolution

2007-11-27 Thread Frenkel, Anatoly
04:44:48 2007 Subject: [Ifeffit] Exafs distance resolution Dear all, Is there a physical limitation determining exafs bond distance resolution? Very often the equation r = pi / 2 deltak is quoted as a measure for bond distance resolution. But as i understand this equation is related to

Re: [Ifeffit] Demeter 0.9.26 launch faillure

2017-12-06 Thread Dardenne, Kathy (INE)
eview version, but I was installing it only to get the possibility to actually use the user-supplied value of epsilon_k for fitting multiple dataset. If it is difficult to make the version 0.9.26 available soon, maybe in 0.9.25 there is a possibility to set R-factor as a figure of merit for fitti

Re: [Ifeffit] Phase correction not working in Athena

2016-08-31 Thread Bruce Ravel
again all caps because this point is so important that I want to yell it at you. THE FOURIER TRANSFORM OF CHI(K) IS NOT A RADIAL DISTRIBUTION FUNCTION. * chi(k) includes multiple scattering * chi(k) includes a complex scattering factor * For heavy elements, the magnitude of the complex sca

[Ifeffit] Regarding a fit for Fe(OTf)2

2014-12-02 Thread pushkar shejwalkar
anticipation Best Pushkar Independent points : 16.125 Number of variables : 4 Chi-square : 7324.9401796 Reduced chi-square : 604.118 R-factor: 0.0195782 Measurement uncertainty (k) : 0.0001264 Measurement uncertainty (R) : 0.0004142

Re: [Ifeffit] Question about PCA

2019-04-25 Thread Matt Newville
inecace...@gmail.com> wrote: > >> Hi Matt, thank you for your answer!. The references I have about >> Malinowski´s work and some applications are: >> >> Malinowski, E.R., *Theory of error in factor analysis.* Analytical >> Chemistry, 1977. *49*(4): p. 606-612. &g

Re: [Ifeffit] Ifeffit Digest, Vol 104, Issue 9

2011-10-09 Thread Soham Mukherjee
first two S subshells are so close to each other, my data can't identify them (delr and ss) independently. So I defined their delr and ss to be same and the results match pretty well with the cubic phase. The r-factor and reduced-chi square with the two models are very similar.Thanks a lot ! O

Re: [Ifeffit] Large Amplitude Values

2010-07-31 Thread Gavin Garside
ly to account for a factor of 2 by normalization if the data is relatively decent. And self-absorption tends to suppress S02, not exaggerate it. Why did you switch to fluorescence on just the handful of data sets? That might provide us a clue. --Scott Calvin Sarah Lawrence College On Jul 30,

[Ifeffit] Fwd: problems by using Artemis and Demeter

2014-07-28 Thread Bruce Ravel
lts in the top of the results window: Later where a summary is usually shown it is left blank: R-factor for this data set = 0.46013 pathdegen amp sigma^2e0reff delta_RR I started a n

Re: [Ifeffit] Hephaestus: Absorption Data Source

2017-11-13 Thread Daniel Przyrembel
of L, M, N, O, and P core levels with binding energies less > than 1500 eV in approximately 25 elements. The results show that the > framework provided by previously accepted theoretical estimates of > lifetime broadening is sometimes misleading. Lifetimes derived from > theory and

Re: [Ifeffit] Data being overwritten in Artemis history window

2015-03-11 Thread Godfrey, Ian
yed > correctly for the most recent fit but, for the previous fit it will have > been overwritten by the newer fit. Some of the other info, such as > R-factor by k-weight seems to get overwritten too. I just pushed a fix for this to github and posted new windows installer candidates at

Re: [Ifeffit] What you see is "not" what you get: help

2009-07-09 Thread Kelly, Shelly
@millenia.cars.aps.anl.gov Subject: [Ifeffit] What you see is "not" what you get: help Hi folks, I´ve been working on Xanes peaks fitting with Athena (last version) and I found a strange behaviour. I get a "good" fit looking to the Graphics Window of Athena and to the minimized parameters (R-f

[Ifeffit] SixPack PCA

2010-04-29 Thread Andrew
work they included standards which had SPOIL values greater than 6, so they would have rejected a standard with a value lower than 6)) 2. Malinowski, E. R., Factor Analysis in Chemistry. Wiley: New York, 2002; p 432. I might be wrong on this but when these programs use the formulas for calculat

Re: [Ifeffit] small-screen version of Athena document

2009-01-26 Thread Frenkel, Anatoly
Bruce and Matt: When Athena and Artemis are completely moved to BlackBerry and iPhone, there will be a number of really nice options out there. For example, ringtones for a really bad fit should be made very unpleasant, and even more so, when Delta E0 is out of bounds, or r-factor is greater

Re: [Ifeffit] Exafs spectra Fitting of WO3 nanoparticles (Abdallah Nassereddine)

2022-08-04 Thread Mosselmans, Fred (DLSLtd,RAL,SCI)
distances from such an analysis is to assert that the difference between the path is a fixed value and thus refine the two paths with the same delta R (and probably the same debye wller factor) this in my experience works in some cases Best regards Fred Mosselmans -Original Message- From

Re: [Ifeffit] Ifeffit Digest, Vol 116, Issue 13

2012-10-23 Thread Tsuei, Ku-Ding
e: Bruce, Perhaps you noticed the "Fit color" was red (large R-factor 0.074496, poor fit, also seen in the attached figure in the last email) when you loaded in the project file I sent you. When you hit Fit button again the "Fit color" might turn to green indicating good fit

Re: [Ifeffit] problems installing athena et al under ubuntu 16.04 LTS

2016-11-25 Thread Matt Newville
, and is not completely reversible. I see a factor of 1000 as a multiplicative factor in the Energy Text Control window when "keV" is selected, but this appears to not be editable. I also see that this only happens when using the Larch backend and not the Ifeffit backend. And, I can als

Re: [Ifeffit] Question about PCA

2019-04-25 Thread Joselaine Cáceres gonzalez
f the Vogt–Mizaikoff F-test to determine the number of principal factors responsible for a data matrix and comparison with other popular methods. Journal of Chemometrics, 2004. 18(9): p. 387-392) is stated that s is equal to r or c, wichever is smaller, in this case s=c, the number of spectra as you said. Y

Re: [Ifeffit] Data being overwritten in Artemis history window

2015-03-09 Thread Jason Gaudet
be displayed correctly in the history window. >> Now change the R window (say 1.5-3.5) and run the fit again. When you go >> to the history window the R window information will be displayed >> correctly for the most recent fit but, for the previous fit it will have >> been

Re: [Ifeffit] Data being overwritten in Artemis history window

2015-03-12 Thread Ravel, Bruce
; this point the log will be displayed correctly in the history window. > Now change the R window (say 1.5-3.5) and run the fit again. When you go > to the history window the R window information will be displayed > correctly for the most recent fit but, for the previous fit it will have >

Re: [Ifeffit] Zinc Sulfide fitting

2011-10-08 Thread JeongEunSuk
hello Two phase can be mixed in ZnS. You need to check r-factor and reduced-chi squrare with two model. If you want to fit only first shell, I suggest. first use cubic zinc-blende model in FEFF, and check goodness of fit. second, fix the bond length of 3 bonding length and change the bond

Re: [Ifeffit] Short questions

2006-09-13 Thread Scott Calvin
is purely made up, as far as I know. It's like saying the fit is pretty close to the data when the EXAFS R-factor is less than 0.02. That 0.02 is arbitrary, but works as a rule of thumb. I myself don't always pay attention to the 2/3 that I have occasionally mentioned. I'm pretty

Re: [Ifeffit] Co fitting questions

2016-09-02 Thread Neil M Schweitzer
work, I got it to the point that the fit looks pretty (R-factor<0.02), but I have several reservations about it: 1) Generally, the ss values are all higher than I would like. 0.007 even seems high to me for a metal-O bond. Am I right about this? Would this indicate that this may have b

Re: [Ifeffit] Ifeffit Digest, Vol 104, Issue 22

2011-10-14 Thread David Sprouster
Julian: I agree with Anatoly. The amplitude of the EXAFS is quite large. I have seen a similar effect in metal foils and NP samples when you forget to take the log of the I0 and IT. This also forces the S02 factor to be artificially high (like it is for your samples) when fitting in Artemis. Maybe

Re: [Ifeffit] Question about transform windows and statistical parameters

2011-05-12 Thread Brandon Reese
the Hanning window I used a dk of 1, and for the K-B window i tried different dk's from 1-5. The kmin and kmax were held constant at 2.5-11. I did notice the large increase in ringing with the low dk values and the K-B window. The fit quality, by R-factor, was substantially worse with

Re: [Ifeffit] Truncating signal

2018-05-10 Thread Julian Ehwald
Hi Matt, Thank you for your answer and for taking time to explain me basic things again and again. I have completely different question as well, and hopefully the last one for a while: I just started using Artemis, and have a question regarding the amplitude reduction factor: I use

Re: [Ifeffit] Linear combination fitting reports

2009-09-02 Thread Bruce Ravel
I tried running a combinatorial LCF series just before writing this email and I think these numbers are reported correctly. If you think otherwise, you will need to show me an example. Of course, the values for both R-factor and reduced chi-square are rather peculiar in Athena's LC fitting, as

Re: [Ifeffit] LCF analysis

2010-10-25 Thread Matthew Marcus
;s saying that there is a 23% that, given the noise level in the data, the fit would indicate that C was present when it was not. That is /not/ the same thing as saying there is a 77% chance of C being present. To see this, imagine very, very noisy data. Including C in the fit might very well i

Re: [Ifeffit] phase problem copper

2015-07-15 Thread Bruce Ravel
On 07/14/2015 10:18 AM, Neeb, Matthias wrote: I have a standard exafs spectrum of copper K-shell and everything looks as expected (Chi(E), Chi(k), Chi(R), Chi(q) …) when using Demeter 0.9.21 . However the phase spectrum of (Chi(q)) appears quite different to literature (e.g. B.K. Teo

Re: [Ifeffit] Problems with EXAFS Fitting of Metalloprotein Zinc Samples

2015-11-10 Thread Bruce Ravel
we think this is strange, because putting 8 imidazoles around a zinc seems kind of silly but it likes it. 5 imidazoles and 3 sulfurs and I have an R-factor of 0.2% every time. If there is non standard multiple scattering that occurs in multiple unrelated proteins from different organisms then w

Re: [Ifeffit] Ifeffit Digest, Vol 111, Issue 5

2012-05-07 Thread Christopher Thomas Chantler
should be included. I remember coming >> across a website that had this information on it awhile ago but I can't >> seem to find my way back. We would like to publish a qualitative XANES >> paper and an EXAFS paper. Any suggestions on the type of information >> (plots, t

Re: [Ifeffit] Ifeffit Digest, Vol 51, Issue 26

2007-05-30 Thread Jun Lin
tistics Number of independent points : 0 Number of variables : 0 Chi-square : 0 Reduced chi-square : 0 R-factor : 0 Measurement uncertainty (k) : 0 Measurement uncertainty (R) : 0 Guess parameters =*==*==*==*==*==*==*==*==*==*==*==*

Re: [Ifeffit] Energy Resolution

2018-05-10 Thread Julian Ehwald
Hi Carlo Thank you for your answer. I have completely different question as well: I just started using Artemis, and have a question regarding the amplitude reduction factor: I use different So^2 for different elements, correct? If I start fitting and have paths involving the same kind of atom but

Re: [Ifeffit] about sigma2 for exafs fitting

2017-01-05 Thread Scott Calvin
list below, then, gives a result of 0.64, which indicates such variation is quite likely to have taken place by chance. You chose the worst case of your three, though; the pH 3 case. The pH 10 case shows the most improvement in the R-factor with x = 0.007/0.012 = 0.58. The probability of getting

Re: [Ifeffit] questions concerning paper

2008-05-22 Thread Matt Newville
home for war, and has many adventures on his way home which might prevent him from ever getting back. Meanwhile, there is a long line of people waiting to take his place at home. > In the next sentence, what is the overall amplitude factor S_0^2? How is > it defined? S_0^2 accounts for the rela

Re: [Ifeffit] Problems with EXAFS Fitting of Metalloprotein Zinc Samples

2015-11-11 Thread Farquhar, Erik
R-space there is no local minima. For Cobalt and Nickel samples I typically get one or a few fits that are obviously significantly better in R-factor (with reasonable distances, sigma^2, etc) but for Zinc this is not the case. I can get many good fits and Zinc likes to increase the coordination up

Re: [Ifeffit] Requesting guidance in understanding results from Athena

2020-09-13 Thread Deepak Varanasi
Good afternoon I understand. In that case, would it be possible for you to perhaps guess the greatest factor causing this problem? My apologies if I may be asking for too much. Yours sincerely Deepak Varanasi On Sun, Sep 13, 2020, 16:39 Deepak Varanasi wrote: > Good afternoon > > T

Re: [Ifeffit] why ss_2 is negative?

2007-02-23 Thread hw26
large compared with the R from literature. But if I force sigma^2 to be positive and e_2 to be below 10 ev, the R-factor will increase and the fitting doesn't seem good. As for the 2.59 Angstrom for equatorial U-O, it is even a little bit larger than the bidentate U-O. I don't think it

Re: [Ifeffit] Question about transform windows and statistical parameters

2011-05-13 Thread Matt Newville
ely change with k, but that would surely be dominated by the rapid decay > in |chi(k)|, rather than a change in epsilon. > > I'm confused. We Fourier transform k-weighted data. Since Ifeffit uses the > high-R amplitude to estimate uncertainty, it seems to me that what matters > i

Re: [Ifeffit] Gold Nanoparticle first shell fitting

2011-10-11 Thread Anatoly I Frenkel
Something is horribly wrong with the data here. I overplotted your reference Au foil against mine, and yours has distorted XANES and too high EXAFS intensity compared to my data. Your amplitude factor is 1.54 which also confirms that something was wrong in the experiment. Perhaps - a

Re: [Ifeffit] Use of the 3rd and 4th Parameter

2014-06-16 Thread Matt Newville
- 0.01) and if I try to do the same with the 4th parameter no fit at all > takes place. The errors in the GDS-window are exactly 0.0 with no fit > taking place (enot = 0, amp = 0 (guess amp = 1) delr = 0 and ss = 0.003) > and the R-factor of the fit is way over the top (>10^20). > >

Re: [Ifeffit] Fwd: Re: why ss_2 is negative?

2007-02-27 Thread Carlo Segre
ep a close eye on the "Reduced Chi-square" as you add more "guess" parameters. If it goes up, you may be overreaching on your model even though the "R-factor" goes down! HTH Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects

Re: [Ifeffit] small-screen version of Athena document

2009-01-26 Thread Richard Mayes
be a number of really nice options out there. For example, > ringtones for a really bad fit should be made very unpleasant, and even more > so, when Delta E0 is out of bounds, or r-factor is greater than 0.02.. > > Anatoly > > -Original Message- > From: ifeffit-

Re: [Ifeffit] Fitting Problems in Artemis version 0.9.26

2018-06-29 Thread Scott Calvin
ersion "Artemis 0.9.26" I have two > problems. (1) The fitting Range was reported to be a error that the Rmin > should be larger than the Rkbg value. It makes that the fitting range cannot > be smaller than 0.9 (the Rkbg value is 0.9). (2) When Fitting the > Debye–Waller fa

[Ifeffit] Analyzing EXAFS data on Artemis

2021-05-27 Thread Alexandros Deltsidis
, namely Li2Se. I try to include a scattering path from the respective Li2Se crystal model in my fits, since a Se (absorber) - Li (backscatterer) pair is present in the R-range of my fit in the Forward Fourier Transform. My question here is if this makes sense since Li is much smaller scatterer

Re: [Ifeffit] What does FEFF stand for?

2011-05-10 Thread Scott Calvin
rocedure in which an effective scattering factor f_eff,j(r,theta_j) which depends on r takes the place of the usual PW [plane wave] f_j(theta_j)." In addition, was FEFF3 a multiple-scattering code? The comments in its header and the 1991 JACS article on it mention only single-scattering. It

Re: [Ifeffit] Asymmetric error bars in IFeffit

2010-10-25 Thread Matt Newville
Hi Scott, That's a pretty amazing use case. But I'm not sure I understand the issue exactly right. I would have thought the volume (r**3) was the important physical parameter, and that a 1000nm particle would dominate the spectra over 3nm particles. Or is it that you are

Re: [Ifeffit] about sigma2 for exafs fitting

2017-01-08 Thread Shaofeng Wang
e most improvement in the R-factor with x = 0.007/0.012 = 0.58. The probability of getting that much improvement by chance drops to 0.30—less likely, but still pretty close to a coin flip. Even the fact that you got all three to show improvement doesn’t quite reach the 95% confidence level, althoug

Re: [Ifeffit] Yttrium in alumina GBs

2006-12-20 Thread Carlo Segre
. In looking at the structures of Al2O3 and Y2O3, I noticed a couple of interesting issues. The first shell in the Al2O3 structure is # Atom R 3 O 1.8519 3 O 1.9717 The Y2O3, however seems to have two diffente Y sites, and the first shells are Site 1

Re: [Ifeffit] amplitude parameter S02 larger than 1

2015-03-20 Thread Anatoly I Frenkel
One possible scenario: If one site has 6 nearest neighbors and the other - 4, and if you choose the site with 4 neighbors to construct FEFF to model your EXAFS data; and if you set your degeneracy equal to 4 and make your amplitude factor as S02*x of one site + S02*(1-x) of another site, then

Re: [Ifeffit] Error in N (Number of Scatterers)

2016-03-09 Thread Matt Newville
cause they are what are typically found in actual analysis of real data. > Several months ago, I wrote to the mailing list regarding the difference > of fitting in R- and k-space in Artemis and received several responses > revealing that some comments made in the Koningsberger rev

Re: [Ifeffit] Co fitting questions

2016-09-02 Thread Carlo Segre
. As you can see, the fit contains four paths. They are all single scattering paths, and the paths with the four largest ranks according to feff. All paths share the same SO2 and deltaE. Each path has its own delR and ss. After some work, I got it to the point that the fit looks pretty (R-factor

Re: [Ifeffit] Inversion Degree

2019-07-05 Thread dcnguyen
atom of Co, you can also calculate the volume fraction in a cubic centimeter of material. To do so, you need to firstly obtain the (short-ranged) lattice parameter (in angstrom) of each phase from an EXAFS fitting with an R-factor less than 0.02. Then the volume (in angstrom cube) of the unit ce

Re: [Ifeffit] Regarding a fit for Fe(OTf)2

2014-12-03 Thread Jason Gaudet
t me know. > Thank you in an anticipation > Best > Pushkar > > > Independent points : 16.125 > Number of variables : 4 > Chi-square : 7324.9401796 > Reduced chi-square : 604.118 > > R-factor:

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