[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 in

[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

Re: [Ifeffit] Different R-factor values

2013-01-25 Thread Bruce Ravel
to implement it. Since fits in Artemis are usually done with multiple k-weights, it wasn't clear to me how to display the information in the clearest manner. The "overall" R factor, the one that Ifeffit reports after the fit finishes, includes all the data and all the k-weights used

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

[Ifeffit] r-factor

2006-06-23 Thread Lisa Giachini
Hi Everyone, 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 for this data set'.

[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 and the

[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 i

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

Re: [Ifeffit] Athena: the R factor for normalized mu(E)

2022-07-13 Thread Matt Newville
Hi Jon Petter, On Tue, Jul 12, 2022 at 12:46 AM Jon-Petter Gustafsson < jon-petter.gustafs...@slu.se> wrote: > Hello all, > > > > I have been a frequent user of Athena for many years, mostly for > interpreting P K-edge XANES spectra. Until last week I thought that the

[Ifeffit] Athena: the R factor for normalized mu(E)

2022-07-11 Thread Jon-Petter Gustafsson
Hello all, I have been a frequent user of Athena for many years, mostly for interpreting P K-edge XANES spectra. Until last week I thought that the R factor in Athena was always defined as: sum( [data_i - fit_i]^2 ) --- sum( data_i^2 ] This is also the

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

2007-01-08 Thread Kelly, Shelly D.
Hi Lisa, In general the R-factor is good if it is less than a few percent. The value reported is 0.01 or 1% then the fit is satisfactory. Just as a note the R-factor is calculated over the entire data range given by rmin and rmax of the fit, so make sure that they are reasonable values. To

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] Different R-factor values

2013-01-25 Thread Jason Gaudet
Perhaps next time I'll notice the attachment ... I don't see that "r factor for k-weight=..." in my old projects; I'm not sure if I just never used that version? I checked some Artemis 0.8.006 logfiles from 2009 and per-k-weight R-factors aren't in there, so tha

Re: [Ifeffit] Consultation on Reduced Chi2

2016-05-23 Thread Jesús Eduardo Vega Castillo
g 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 of 3039 and >> R-factor of 0.00

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.

[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 of

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

2012-03-10 Thread Matt Newville
re 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

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

2007-03-06 Thread Scott Calvin
very dilute 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

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

[Ifeffit] Per-data set R-factor

2012-12-20 Thread Lyle Gordon
Dear iffefit users, I am using the latest version of Demeter/Artemis to fit some EXAFS data. I'm running Win 7 64. I found in Horae that when I fit multiple datasets it would output the R-factor for each dataset in the fit. I would really like these values in the newest version. I found o

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 calculatio

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

[Ifeffit] error

2011-01-11 Thread JeongEunSuk
was fitting, there are only 8 parameters in both two method. So that independent data point and variables are same. Both 1st and 2nd had same R-factor but reduced chi-square of 1st was lager than that of 2nd. It has been known that R-factor is independent of error( uncertainty in the measurement

[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 208&209 (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 (imagi

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 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 (&

Re: [Ifeffit] Different R-factor values

2013-01-25 Thread Matt Newville
rrect me on this, but if I remember right there were > individual-data-set R-factor and chi-square calculations at some point, > which come not from IFEFFIT but from Bruce's own post-fit calculations, and > these eventually were found to be pretty buggy and were dropped. > > I don

Re: [Ifeffit] error

2011-01-11 Thread Matt Newville
meters for Mg like bonding length, disorder and others were set. > When I was fitting, there are only 8 parameters in both two method. So that > independent data point and variables are same. > > Both 1st and 2nd had same R-factor but reduced chi-square of 1st was lager > than that o

Re: [Ifeffit] ifeffit R-factor

2013-04-07 Thread Matt Newville
Hi Sandra, On Sat, Apr 6, 2013 at 12:37 PM, Sandra Luber 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] Ifeffit Digest, Vol 119, Issue 19

2013-01-15 Thread Denis Testemale
Hello Chris. - I don't have an answer regarding the R-factor. - Noise or glitch: how does I0 look like? Is the glitch you suspect visible in I0 at this energy? If you're refering to the feature that points downwards at 8A-1, it actually shifts with the spectra (I can see two groups

[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

[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 d

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. the

[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] Chi in arthemis

2009-08-18 Thread Scott Calvin
dations by not reporting chi-square. Of course, I tend to work in circumstances where the signal-to-noise ratio is very high, and thus the statistical uncertainties make a very small contribution to the overall measurement error. In such cases I have become convinced that the R-factor alone p

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

2012-03-10 Thread Matt Newville
effit/2005-October/006613.html > http://cars9.uchicago.edu/ifeffit/FAQ/FeffitModeling > > I am waiting also for the answer from authors I would have said these questions have been answered, but maybe I misunderstand... What is the question you are waiting to be answered? All of chi-square

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 (&

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

Re: [Ifeffit] Per-data set R-factor

2012-12-21 Thread Bruce Ravel
data. I'm running Win 7 64. > > I found in Horae that when I fit multiple datasets it would output the > R-factor for each dataset in the fit. I would really like these values > in the newest version. > > I found on the todo list > (https://github.com/bruceravel/demeter

[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
hi-square : 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 * *

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 C

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
06613.html http://cars9.uchicago.edu/ifeffit/FAQ/FeffitModeling I am waiting also for the answer from authors I would have said these questions have been answered, but maybe I misunderstand... What is the question you are waiting to be answered? All of chi-square, reduced chi-square, and R factor e

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

2012-03-10 Thread Matt Newville
our model of the data is much better than that data > uncertainty. Many people describe these as "systematic errors" and > include alll sorts of data processing artifacts as well as errors in > the Feff calculations. > > For us, reduced chi-square is almost always >>

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

2012-10-21 Thread Ravel, Bruce
quare =4334.684537717 Reduced Chi-square = 691.819976095 R-factor= 0.004250325 amp = 0.8649100 +/- 0.0412220(1.) enot= 5.6049380 +/- 0.2950270(0.) delr=-0.02

Re: [Ifeffit] Chi in arthemis

2009-08-18 Thread Matthew
hat should be reported, I do deviate from the IXAS > recommendations by not reporting chi-square. Of course, I tend to work > in circumstances where the signal-to-noise ratio is very high, and > thus the statistical uncertainties make a very small contribution to > the overall measure

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

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
rt 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 para

Re: [Ifeffit] Cadmium K-edge

2011-01-09 Thread Alan Du
ing like 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) = 0.6042

Re: [Ifeffit] N independent variables

2016-05-23 Thread Jesús Eduardo Vega Castillo
: 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 = 2.94

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

2021-03-26 Thread Ava Rajh
Chi-square : 0.000 Reduced chi-square : 0.000 R-factor: 0.000 Number of data sets : 1 Happiness = 100.00/100 color = #D8E796

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

2012-10-22 Thread Bruce Ravel
26 AM Tsuei, Ku-Ding wrote: > 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

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

2013-01-15 Thread Scott Calvin
ange ( k = 2-7 and R = 1-2) really constrains the model > Nidp = 3.31. Luckily, multiple datasets ( 8 ) to the rescue to give me > some flexibility. In a multiple dataset fitting, is the R-factor of the > whole set just the average or total mismatch across all the data

Re: [Ifeffit] Chi in arthemis

2009-08-19 Thread Matt Newville
dels with different 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 b

[Ifeffit] Questions on Correlated Debye in FEFF6

2015-06-11 Thread Bennett, Doran (D)
th, 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 sinc

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-f

[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

[Ifeffit] "FEFF+IFEFFIT" and "cumulant expansion+ratio method" approaches

2006-07-09 Thread Leandro Araujo
ho(r)" distributions of interatomic distances, which are related by: P(r,lambda)=rho(r)*[[exp(-2r/lambda)]/r^2] . For the second cumulant (Debye-Waller factor or sigma^2) and higher terms, the difference between "effective" and "real" values is not significant unless the

Re: [Ifeffit] third cumulant

2012-05-07 Thread Matt Newville
de exact bonding length and third culmulant because their correlation. I think that the relation of both bonding length and third culmulant is similar to that of number and debye-waller factor. > Is it right to find bonding length and third culmulant like finding number and debye-waller factor usin

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

2020-03-30 Thread t . zahoransky
ables, 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

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

2012-10-23 Thread wangshaofeng
> > > On Monday, October 22, 2012 06:41:26 AM Tsuei, Ku-Ding wrote: > > 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

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" wrote: > On Friday, April 0

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 th

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

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

[Ifeffit] Writing a paper

2012-05-07 Thread mattie.p...@huskers.unl.edu
ish 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 If

[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

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

2012-01-12 Thread Kropf, Arthur Jeremy
05100 //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

[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

[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 for the

Re: [Ifeffit] Consistency criterion

2006-09-28 Thread Scott Calvin
Hi Juan, They're consistent. The higher r-factor on the kwt-1 data might be a clue about how reliable part of your data range is...since it's the kwt-1 that's higher, it may be that the low end of the k-range is not being fit very well (look at the k-space and q-space fits t

Re: [Ifeffit] Trouble with fitting with Arthemis

2009-01-13 Thread Scott Calvin
hat is > happening? > > > Independent points = 8.239257812 > Number of variables = 1.0 > Chi-square = 0.12000E+37 > Reduced Chi-square = 0.165762849E+36 > R-factor=

Re: [Ifeffit] Trouble with fitting with Arthemis

2009-01-13 Thread Bruce Ravel
257812 > 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 (R)

[Ifeffit] Data being overwritten in Artemis history window

2015-03-09 Thread Godfrey, Ian
ly 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. A video of this behaviour can be found here: https://wwwa-e.ucl.ac.uk/cgi-bin/dropbox/dropbox.cgi?state=pickup_i

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

2015-03-09 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. Ian, I now understand what the problem is. Unhappily, it is the result of a fairly deep mistake in how the history feature of Artemis works. I should

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

2007-06-28 Thread Matt Newville
you would consider following Bruce's 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 an

[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 e

[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 of not

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

2012-01-13 Thread Kropf, Arthur Jeremy
background k -range = 2.5 ~ 15, EO=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 nu

Re: [Ifeffit] Co fitting questions

2016-09-02 Thread Carlo Segre
Hi Neil: I took your data and fit it with the Co(OH)2 structure but only the first two paths: Co-O and Co-Co. I used a k-range of 2-10 and dk=3 and the r-range of 1-3.5 with dr=0.2. The fit results are as follows R-factor= 0.024528565 Guess parameters

Re: [Ifeffit] Exafs distance resolution

2007-11-27 Thread Matt Newville
le, FFTs in Ifeffit+Friends use a k-space grid of 0.05Ang^-1 and kmax of 102.4Ang^-1, and a grid in R-space of ~0.03Ang. This would limit resolution to about ~-0.03Ang, which might be a limiting factor if you have data to k~=50Ang^-1. It probably limits precision too, though I do not know t

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 t

Re: [Ifeffit] Co fitting questions

2016-09-02 Thread Neil M Schweitzer
(both R-factor and Reduced chi-square are reduced). However, now the SO2 is ~1.11. Does this make physical sense? What would be the cause of it being too big? Neil -Original Message- From: Ifeffit [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Carlo Segre Sent: Friday

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

2015-03-09 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. A video of this behaviour can be found here: https://wwwa-e.ucl.ac.uk/cgi-bin/dropbox/dropbox.cgi?state=pickup_info&id=29d3e5c2 password: 54c8545f S

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 for

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 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 / ∑( > chi_E(ki))2] ? > > Where

Re: [Ifeffit] Questions on Correlated Debye in FEFF6

2015-06-19 Thread Bruce Ravel
From 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 t

[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] Negative ss problem

2010-07-14 Thread Chris Patridge
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] Sixpack, PCA controll, "IND" column

2012-06-21 Thread Baker, Leslie
ack paper cites Malinowski's 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. -L

Re: [Ifeffit] Writing a paper

2012-05-07 Thread Bruce Ravel
on 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, tables, R-factor, etc.) that should be included in each paper > separately would be apprecia

Re: [Ifeffit] Cadmium K-edge

2011-01-10 Thread Bhoopesh Mishra
O3). No multiple > scattering paths used. The best fit goes something like this: > > > > Independent points = 13.166992187 > Number of variables = 8.0 > Chi-square =1534.709946959 > Reduced Chi-square

Re: [Ifeffit] Estimation of S02

2008-10-08 Thread Leandro Araujo
is not the straight answer 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 2008/10/9 Hiroshi O

Re: [Ifeffit] Trouble with fitting with Arthemis

2009-01-13 Thread Kleper Oliveira Rocha
-1. +/- 0.00 like example down. What is happening? > > > > > > Independent points = 8.239257812 > > Number of variables = 1.0 > > Chi-square = 0.12000E+37 > > Reduced Chi-square

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 for

Re: [Ifeffit] Questions on Correlated Debye in FEFF6

2015-06-19 Thread Matt Newville
; > > 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 in the Debye spectral > density? It seems like it would not be reasonable to tre

Re: [Ifeffit] Energy shift

2011-10-05 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] Manuscript comments regarding EXAFS modeling

2021-08-29 Thread Matt Newville
but it does not lower correlations between N and sigma2 (or E0 and R) by very much. Cheers, On Fri, Aug 27, 2021 at 7:41 PM Peng Liu wrote: > Dear Ifeffit members, > > I received the following two comments. > > " > Comment 1: Authors have fixed the amplitude reduction facto

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