[Ifeffit] R-factor uncertainty

2007-01-05 Thread Lisa Giachini
Dear all, I have a question about the R factor: how can I decide if the difference between the R factors of 2 fits is statistically significant, i.e, how can I calculate the uncertainty which has to be associated to the R factor? B.R., Lisa

[Ifeffit] Different R-factor values

2013-01-24 Thread Christopher Patridge
Hello List, I know that Horae is no longer supported but I had quick question about the R-factor. I search the mailing list and found this post from 2006 concerning different R-factors in the fit log I have a question about Artemis log file. I noticed that two r-factors are reported

Re: [Ifeffit] Find R-factor for linear combination sums?

2012-01-08 Thread Scott Calvin
Thanks, Matt, I'll give it a try. --Scott On Jan 8, 2012, at 10:06 PM, Matt Newville wrote: It should be possible to calculate an R-factor or chi-square statistics with a fairly simple ifeffit macro, using the functions vsum() (to sum an array) and npts

[Ifeffit] Consultation on Reduced Chi2

2016-05-23 Thread Jesús Eduardo Vega Castillo
Dear list, I am back with a new consultation on EXAFS fitting within Artemis. I have made a fit and obtained a reduced Chi2 value of 391 and R-factor of 0.014 using 9 variables. Then I have added two more paths increasing the number of variables up to 12 and then I obtained a reduced Chi2

[Ifeffit] Fwd: Re: r-factor

2006-06-23 Thread Bruce Ravel
On Friday 23 June 2006 05:01, you wrote: I have a question about Artemis log file. I noticed that two r-factors are reported in the log file. One is in the fifth line and it is called 'R-factor'  and the other one is under the data set fitting conditions and it is called 'r-factor

[Ifeffit] Calculation of NSS and R-factor

2017-05-16 Thread Marine Albertelli
Good afternoon, Could you please tell me what is the difference between the calculation of the R-factor and the NSS ? I found that R-factor is equal to : sum((data - fit)^2)/sum(data^2) and NSS = sum((data - fit)^2)/sum(data^2)*100 But when I compare the R-factor obtained by Athena

Re: [Ifeffit] Calculation of NSS and R-factor

2017-05-16 Thread Matt Newville
Hello Marine, On Tue, May 16, 2017 at 4:59 AM, Marine Albertelli < marine.alberte...@univ-pau.fr> wrote: > Good afternoon, > > Could you please tell me what is the difference between the calculation of > the R-factor and the NSS ? > > I found that R-factor is equal to :

Re: [Ifeffit] R-factor uncertainty

2007-01-05 Thread Scott Calvin
Hi Lisa, At 07:23 AM 1/5/2007, you wrote: I have a question about the R factor: how can I decide if the difference between the R factors of 2 fits is statistically significant, i.e, how can I calculate the uncertainty which has to be associated to the R factor? As I understand it, you

Re: [Ifeffit] Chi in arthemis

2009-08-18 Thread Matt Newville
Dear Eugenio, I see that the R-factor is pretty good, 1.74%, amp is high cause is correlated with the coordination number and always have big errors., delr has the error of the total distance, so it is ok, but ss and enot have a a really big error, is this normal? What leads you to conclude

[Ifeffit] Chi in arthemis

2009-08-18 Thread Eugenio Otal
Hi Scott, here I copy a part of the report: Independent points = 6.222656250 Number of variables = 4.0 Chi-square = 247.145092496 Reduced Chi-square = 111.193574128 R-factor= 0.017422216 Guess

Re: [Ifeffit] Consultation on Reduced Chi2

2016-05-23 Thread Matt Newville
Jesus, On Mon, May 23, 2016 at 7:08 AM, Jesús Eduardo Vega Castillo < jeve...@gmail.com> wrote: > Dear list, > > I am back with a new consultation on EXAFS fitting within Artemis. > > I have made a fit and obtained a reduced Chi2 value of 391 and R-factor of > 0.014 u

Re: [Ifeffit] Consultation on Reduced Chi2

2016-05-23 Thread Jesús Eduardo Vega Castillo
a new consultation on EXAFS fitting within Artemis. >> >> I have made a fit and obtained a reduced Chi2 value of 391 and R-factor >> of 0.014 using 9 variables. Then I have added two more paths increasing the >> number of variables up to 12 and then I obtained a reduced Chi2

Re: [Ifeffit] Find R-factor for linear combination sums?

2012-01-08 Thread Matt Newville
Hi Scott, On Sat, Jan 7, 2012 at 12:42 PM, Scott Calvin scal...@sarahlawrence.edu wrote: Hi all, Is there a way to get Athena (or Ifeffit) to report an R-factor for a linear combination sum, as opposed to a fit? Artemis does that for FEFF fitting, and Athena will do a linear combination

Re: [Ifeffit] (no subject)

2013-03-13 Thread Bruce Ravel
On Wednesday, March 13, 2013 08:24:41 PM davood dar wrote: 1. *1*.What is the ideal value of R- factor for any fit. R-factor is a way of expressing percentage misfit. Smaller is generally better, although smaller is not better if other aspects of the fit are not defensible

Re: [Ifeffit] Different R-factor values

2013-01-25 Thread Christopher Patridge
Thank you for the discussion Matt and Jason, My main objective was to decide between the two different reported R-factors in some older Artemis fit file logs. I suspect that the analysis was prematurely completed because the user found small R-factor values printed out along with the other

[Ifeffit] Query regarding error bars

2009-01-09 Thread Bindu R.
Hi all,   Could any tell me in a simple language about the error bars returned by the EXAFS fitting program?   what do they exactly represent?How is it determined?How is the number of iterations decided.In addition to R-factor what are the other parameters which

[Ifeffit] R quality factor in k space

2009-04-17 Thread Cammelli Sebastiano
Dear iffefit user, I found on a paper (E.A. Stern et al. /Physica B 208209 (1995) 117 120) the definition of R quality factor as: R_factor ≡ ∆chi(R space)) = √[ ∑ |chi_C(Ri) – chi_E(Ri)|2 / ∑( chi_E(Ri))2] formula 3 Where Chi(Ri) is a complex function (imaginary and real part

Re: [Ifeffit] ifeffit R-factor

2013-04-07 Thread Matt Newville
Hi Sandra, On Sat, Apr 6, 2013 at 12:37 PM, Sandra Luber s.lu...@pci.uzh.ch wrote: Dear Matt Newville, I do some fitting with ifeffit using EXAFS data generated by feff. I wonder how the R-factor is calculated. Unfortunately, I have not found any definition yet. Would it be possible

Re: [Ifeffit] Different R-factor values

2013-01-25 Thread Jason Gaudet
Hi Chris, Might be helpful also to link to the archived thread you're talking about. http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2006-June/007048.html Bruce might have to correct me on this, but if I remember right there were individual-data-set R-factor and chi-square calculations

Re: [Ifeffit] running ifeffit under 64-bit windows7

2012-03-10 Thread Matt Newville
artifacts as well as errors in the Feff calculations. For us, reduced chi-square is almost always 1, unless the data is very noisy. R-factor scales the fit residual by the magnitude of the data itself, for some estimate of fractional misfit. This gives a convenient measure that is independent

Re: [Ifeffit] running ifeffit under 64-bit windows7

2012-03-10 Thread Matt Newville
are slightly different, I have appended the message with these results. the very low value of R-factor produced with the 64bit system is difficult to interpret. the questions are; 1- how to account for these differences? 2- if I to publish something, which measure of the quality should I present? and how

Re: [Ifeffit] Artemis

2006-11-10 Thread Juan Antonio Macia Agullo
OK, good answer Scott. My fits have lower values of R-factor but when I depict them in k-space they do not fit quite well to the experimental data due to the short range of R space chosen, of course if I increase range of R then I hope fits in k space will look better. When I talked about

Re: [Ifeffit] Chi in arthemis

2009-08-18 Thread Scott Calvin
points = 6.222656250 Number of variables = 4.0 Chi-square = 247.145092496 Reduced Chi-square = 111.193574128 R-factor= 0.017422216 Guess parameters +/- uncertainties (initial guess): amp

[Ifeffit] Writing a paper

2012-05-07 Thread mattie.p...@huskers.unl.edu
a qualitative XANES paper and an EXAFS paper. Any suggestions on the type of information (plots, tables, R-factor, etc.) that should be included in each paper separately would be appreciated. Thanks, Matthea Peck ___ Ifeffit mailing list Ifeffit

[Ifeffit] Find R-factor for linear combination sums?

2012-01-07 Thread Scott Calvin
Hi all, Is there a way to get Athena (or Ifeffit) to report an R-factor for a linear combination sum, as opposed to a fit? Artemis does that for FEFF fitting, and Athena will do a linear combination sum (plot data + sum with weights entered into the LCF standards boxes), but I don't see a way

Re: [Ifeffit] Find R-factor for linear combination sums?

2012-01-07 Thread Bruce Ravel
On Saturday, January 07, 2012, 01:42:43 pm, Scott Calvin wrote: Hi all, Is there a way to get Athena (or Ifeffit) to report an R-factor for a linear combination sum, as opposed to a fit? Artemis does that for FEFF fitting, and Athena will do a linear combination sum (plot data + sum

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

2007-03-06 Thread Scott Calvin
fluorescence, it's reasonable to expect statistical effects to inflate the R-factor a bit.) R-factor 0.10: Serious problems with the fit. The underlying model may be incorrect. It's best at this stage to look at the spectrum for clues. Maybe the wiggles are qualitatively right, but shifted over

Re: [Ifeffit] N independent variables

2016-05-23 Thread Matt Newville
ts : 17.7666016 > Number of variables : 17 > Chi-square : 265.0947132 > Reduced chi-square : 345.8050781 > > R-factor: 0.0026486 > > Number of data sets : 1 > : k-range = 2.942 - 1

Re: [Ifeffit] running ifeffit under 64-bit windows7

2012-03-10 Thread Dr. Dariusz A. Zając
foil with the two diffrent machines, a 32 bit and 64 bit ones, both running widows7, 32 ans 64 bit respectively. The results obtained are slightly different, I have appended the message with these results. the very low value of R-factor produced with the 64bit system is difficult to interpret

[Ifeffit] N independent variables

2016-05-23 Thread Jesús Eduardo Vega Castillo
: 345.8050781 R-factor: 0.0026486 Number of data sets : 1 : k-range = 2.942 - 11.043 : dk= 1 : k-window = hanning : k-weight = 1,2,3 : R-range = 1.115 - 3.5 : dR= 0.0 : R-window

Re: [Ifeffit] running ifeffit under 64-bit windows7

2012-03-10 Thread Matt Newville
-square, and R factor express the sum of squares of the residual (data-model) after a fit has finished.  The difference between these statistics is how they are scaled. In particular, chi-square is scaled by the estimated error in the data. If you look at a (naive?) introduction to statistics

Re: [Ifeffit] Third cumulant in DWF

2011-04-04 Thread Ping, Yuan
Thanks, Bruce. Does the math expression in IFEFFIT include the term -4k*sigma2*(1/labmda +1/R) in the phase? If yes, the 1st cumulant is sigma1= R+dR. If no, sigma1= R+dR+2*sigma2*(1/labmda +1/R). It this correct? Yuan On 4/1/11 2:18 PM, Bruce Ravel bra...@bnl.gov wrote: On Friday, April 01

Re: [Ifeffit] Query regarding error bars

2009-01-09 Thread Kelly, Shelly
program?   what do they exactly represent?How is it determined?How is the number of iterations decided.In addition to R-factor what are the other parameters which determines a good fit.For a R-factor ~0.001, if the value of chi2~10,000 and reduced chi2 ~ 500

[Ifeffit] path contribution to fit in low R-space position, but the fit bond length is much longer than that

2014-07-01 Thread ZHAN Fei
: 756.5273522 R-factor: 0.0023036 Measurement uncertainty (k) : 0.0002947 Measurement uncertainty (R) : 0.0004735 Number of data sets : 1 Happiness = 100.00/100 color = #D8E796 * Note: happiness is a semantic parameter and should * *NEVER

Re: [Ifeffit] Running (D)Artemis yields different result from that shown in (D)Artemis instruction videos

2012-10-21 Thread Ravel, Bruce
=4334.684537717 Reduced Chi-square = 691.819976095 R-factor= 0.004250325 amp = 0.8649100 +/- 0.0412220(1.) enot= 5.6049380 +/- 0.2950270(0.) delr=-0.0226780

[Ifeffit] Questions about Athena and XANES

2008-02-20 Thread Jenny Cai
Hi all, Could someone please answer my questions? I would really appreciate your help. 1. For linear combination fitting, there are three indicators for the goodness of fitting: R-factor, chi-square and reduced chi-square. Could anyone tell me how they work? 2. Since TEY is sensitive

[Ifeffit] (no subject)

2013-03-13 Thread davood dar
Respected Sir, I am new in the field of EXAFS. I have few questions regarding to IFEFFIT i.e., fitting of theoretical models to the experimental EXAFS data. 1. *1*.What is the ideal value of R- factor for any fit. 2. *2. * Can we use (fit) the theoretical model

[Ifeffit] questions regarding to ifeffit fitting

2013-03-13 Thread davood dar
Respected Sir, I am new in the field of EXAFS. I have few questions regarding to IFEFFIT i.e., fitting of theoretical models to the experimental EXAFS data. 1. What is the ideal value of R- factor for any fit. 2. * * Can we use (fit) the theoretical model generated from

[Ifeffit] questions related to ifeffit fitting

2013-03-14 Thread davood dar
Respected Sir, I am new in the field of EXAFS. I have few questions regarding to IFEFFIT i.e., fitting of theoretical models to the experimental EXAFS data. 1.What is the ideal value of R- factor for any fit. 2. ** Can we use (fit) the theoretical model generated from

Re: [Ifeffit] Query regarding error bars

2009-01-09 Thread Bruce Ravel
On Friday 09 January 2009 09:12:16 am Bindu R. wrote: Could any tell me in a simple language about the error bars returned by the EXAFS fitting program? what do they exactly represent? How is it determined? How is the number of iterations decided. In addition to R-factor what are the other

Re: [Ifeffit] Cadmium K-edge

2011-01-09 Thread Alan Du
this: Independent points = 13.166992187 Number of variables = 8.0 Chi-square =1534.709946959 Reduced Chi-square = 297.021921317 R-factor= 0.000128095 Measurement uncertainty (k) = 0.60423 Measurement

Re: [Ifeffit] N independent variables

2016-05-23 Thread Jesús Eduardo Vega Castillo
t; Independent points : 17.7666016 >> Number of variables : 17 >> Chi-square : 265.0947132 >> Reduced chi-square : 345.8050781 >> >> R-factor: 0.0026486 >> >> Number of data sets : 1 >> :

Re: [Ifeffit] k-range question R-factor

2013-01-15 Thread Christopher Patridge
Thank you Scott, I guess that is a refinement of my question concerning R-factor.' Chris Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501 On 1/15/2013 9:39 AM, Scott Calvin

Re: [Ifeffit] Chi in arthemis

2009-08-19 Thread Matt Newville
number of variables. Many analysis programs report only a value like R-factor (ie, the misfit not scaled by the measurement uncertainty or number of free parameters in the data). Again, this is an OK measure of the misfit, though it too is scaled somewhat arbitrarily, and cannot be used to compare

[Ifeffit] Questions on Correlated Debye in FEFF6

2015-06-11 Thread Bennett, Doran (D)
, is the magnitude of the DW factor determined by assuming the total path length R is the appropriate length to use for the correlation term in the Debye spectral density? It seems like it would not be reasonable to treat all paths of the same R as having the same Debye-Waller factor since a single

Re: [Ifeffit] Running (D)Artemis yields different result from that shown in (D)Artemis instruction videos

2012-10-21 Thread Tsuei, Ku-Ding
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 as shown in your result

[Ifeffit] Trouble with fitting with Arthemis

2009-01-13 Thread Kleper Oliveira Rocha
points = 8.239257812 Number of variables = 1.0 Chi-square = 0.12000E+37 Reduced Chi-square = 0.165762849E+36 R-factor= NaN Measurement uncertainty (k) = 0.000437667 Measurement uncertainty

Re: [Ifeffit] Trouble with fitting with Arthemis

2009-01-13 Thread Scott Calvin
? Independent points = 8.239257812 Number of variables = 1.0 Chi-square = 0.12000E+37 Reduced Chi-square = 0.165762849E+36 R-factor= NaN Measurement uncertainty (k

Re: [Ifeffit] a question

2009-08-25 Thread Jason Gaudet
Are you determining bond length from the magnitude of chi(R) or are you fitting ab initio data to the curves? In my experience the |chi(R)| peaks are usually closer than the actual bond distances due to phase shift. Dr Somaditya Sen wrote: Hi All I am having problems in comparing the real

Re: [Ifeffit] Negative ss problem

2010-07-14 Thread Chris Patridge
is trying to compensate for high R space magnitude by making amp above 1 and ss negative. Have you considered your data processing in Athena? Did you use the default settings? I would guess Cu-O bonds might be too short for the presets in Athena. How did you check your model? Buena salud

Re: [Ifeffit] Fwd: scattering amplitude by FEFF and Artemis

2007-06-28 Thread Matt Newville
suggestion of sending a project file. For what it's worth (in case you missed it while you were reading the docs and tutorials), |chi(q)| = magnitude of the complex chi(q) = FT^(-1) [ chi(R) * Window(R) ] where Window(R) is a Windowing function and chi(R) = FT[ chi(k) * k^w * Window(k) ] where

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

2015-03-09 Thread Bruce Ravel
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. A video of this behaviour can be found here: https://wwwa-e.ucl.ac.uk/cgi-bin/dropbox/dropbox.cgi?state=pickup_infoid=29d3e5c2 password: 54c8545f System info: Win 8.1

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

2015-03-10 Thread Bruce Ravel
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 other questionable

[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

[Ifeffit] Linear Combination Fitting - More Questions

2008-07-17 Thread Gudrun Lisa Bovenkamp
it 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] R quality factor in k space

2009-04-17 Thread Matt Newville
On Fri, Apr 17, 2009 at 8:08 AM, Cammelli Sebastiano sebastiano.camme...@psi.ch wrote: In the case of a linear combination fitting on the k space performed by ATHENA, the ∆chi needs a correction. Is it correct to write: R_factor ≡ ∆chi(k space)) = √[ ∑ (chi_C(ki) – chi_E(ki))2 / ∑(

Re: [Ifeffit] LCF analysis

2010-10-25 Thread Scott Calvin
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 that should lead

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

2012-06-29 Thread Bruce Ravel
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 understanding your explanation, but it seems as though you

[Ifeffit] S02 and k_min

2012-12-02 Thread Michael Morrill
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 of the fit (R-factor from 0.028 to 0.009), but also increases S02. If I use a large enough

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

2014-06-16 Thread Michael Kömm
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 shell fit

[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] Problems with EXAFS Fitting of Metalloprotein Zinc Samples

2015-11-10 Thread Carolyn Carr
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 we would have no idea what this could be. Thanks for your comments! Carolyn Carr

[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 c

Re: [Ifeffit] Questions about Athena and XANES

2008-02-20 Thread Matt Newville
Hi Jenny, 1. For linear combination fitting, there are three indicators for the goodness of fitting: R-factor, chi-square and reduced chi-square. Could anyone tell me how they work? This is actually documented in Athena, and the Users Guide. They are also defined in the Feffit documentation

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

2012-01-12 Thread Kropf, Arthur Jeremy
//Debye waller factor 2. fitting results fit results, goodness of fit, and error analysis: independent points in data= 8.152 number of variables in fit= 3 degrees of freedom in fit = 5.152 r-factor of fit = 0.002700 chi

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] Problems with EXAFS Fitting of Metalloprotein Zinc Samples

2015-11-09 Thread Carolyn Carr
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 have ever fit, although there is obviously no physical basis in this. This is true

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

2009-06-22 Thread Zajac, Dariusz A.
# - # 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

Re: [Ifeffit] Energy shift

2011-10-06 Thread Dr. Dariusz A. Zając
0.003047 r-factor: 11 reduced-chi square: 95 Energy shift by fit shows an amount of difference from Pt L3 edge. It is my problem. To reduce the energy shift, I tried to remove background carefully again and to change distance Pt-O. However the result was failed

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 sensitive that TEY

Re: [Ifeffit] Sixpack, PCA controll, IND column

2012-06-21 Thread Baker, Leslie
1977 paper, and both are available online. S M Webb (2005) SIXpack: a graphical user interface for XAS analysis using IFEFFIT. Phys. Scr. T115, 1011. E R Malinowski (1977) Determination of the Number of Factors and the Experimental Error in a Data Matrix. Anal Chem 49, 612. -Leslie -Original

Re: [Ifeffit] Questions on Correlated Debye in FEFF6

2015-06-19 Thread Bruce Ravel
the Larch manual: http://cars.uchicago.edu/xraylarch/xafs/feffpaths.html#models-for-calculating 2. Assuming the DW factors are calculated path-by-path, is the magnitude of the DW factor determined by assuming the total path length R is the appropriate length to use for the correlation term

Re: [Ifeffit] Running (D)Artemis yields different result from that shown in (D)Artemis instruction videos

2012-10-23 Thread wangshaofeng
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 as shown in your result of a much

Re: [Ifeffit] Trouble with fitting with Arthemis

2009-01-13 Thread Bruce Ravel
= 1.0 Chi-square = 0.12000E+37 Reduced Chi-square = 0.165762849E+36 R-factor= NaN Measurement uncertainty (k) = 0.000437667 Measurement uncertainty (R) = 0.000724906 Number of data sets

Re: [Ifeffit] Trouble with fitting with Arthemis

2009-01-13 Thread Kleper Oliveira Rocha
? Independent points = 8.239257812 Number of variables = 1.0 Chi-square = 0.12000E+37 Reduced Chi-square = 0.165762849E+36 R-factor= NaN Measurement uncertainty (k

[Ifeffit] About export Chi(K) file

2010-02-03 Thread 康明亮
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 peak fitted perfectly. Thus, I am not sure how many path that I should choose for fitting(I know only path

Re: [Ifeffit] Multiple data set fit limit

2017-03-09 Thread Victor Streltsov
Artemis gives me message “ -- falling back to Ifeffit”. I assume it runs Ifeffit which does exactly what Bruce described: 3 data set refined to completion with sensible refined parameter, however, R-factor for 3rd data set is 1. (overall R for 3 data set is huge too) and after-fit plot

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 12nb! sp; Pt atoms

Re: [Ifeffit] weighting multi-data fit

2007-06-20 Thread Jörg Haug
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 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

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 reduced chi

Re: [Ifeffit] Cadmium K-edge

2011-01-10 Thread Bhoopesh Mishra
this: Independent points = 13.166992187 Number of variables = 8.0 Chi-square =1534.709946959 Reduced Chi-square = 297.021921317 R-factor= 0.000128095 Measurement uncertainty (k

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, the beauty of both

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

2011-05-13 Thread Scott Calvin
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 sure there wasn't something odd about this particular chi(k), I took one of the data sets included with the horae distribution: the fil

Re: [Ifeffit] Using windows apj files on linux

2007-05-30 Thread Ravel, Bruce D.
: 0 Reduced chi-square : 0 R-factor : 0 Measurement uncertainty (k) : 0 Measurement uncertainty (R) : 0 Guess parameters

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] 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] 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] Asymmetric error bars in IFeffit

2010-10-24 Thread Frenkel, Anatoly
Scott, It is a strange result. Suppose you fit a bulk metal foil and vary the 1nn coordination number. You will not get 12 +/- 1000. You will get about 12 +/- 0.3 depending on the data quality and the k range, and on the amplitude factor you fix constant. Then, suppose you take your formula

[Ifeffit] save Artemis project and cannot find Path List information when reopen

2014-08-28 Thread huyanyun
-factor: 0.0266456 Measurement uncertainty (k) : 0.0007222 Measurement uncertainty (R) : 0.0017191 Number of data sets : 1 Happiness = 87.35/100 color = #F6EC91 An R-factor of 0.02665 gives

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 for the fit

[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

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

2007-02-27 Thread Carlo Segre
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, Graduate College Illinois Institute of Technology

Re: [Ifeffit] Exafs distance resolution

2007-11-27 Thread Frenkel, Anatoly
Nov 27 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

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] LCF analysis

2010-10-25 Thread Wayne W Lukens Jr
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--maybe, in fact, there's a 45% chance

Re: [Ifeffit] calculating particle size from coordination numbers

2013-10-31 Thread Bruce Ravel
coordination number to the bulk coordination number via particle radius? (equation 4) How can I do this in Artemis when there's other variables such as deltaE, debye-waller factor and delr to worry about? This is the central problem of EXAFS analysis, or indeed of any non-linear analysis. Artemis reports

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] 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] Demeter 0.9.26 launch faillure

2017-12-06 Thread Dardenne, Kathy (INE)
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 Lomachenko -- Dr. Kirill A. Lomachenko Scientist at BM23/ID24 beamlines European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs CS 4022

  1   2   3   >