Re: [Ifeffit] Plot multiple fits in (D)Artemis and statistical errors
Nilmar, First off, sorry I did not respond to this part of your email earlier. Life has been busy for me lately. Today I am going over items in the mailing list from the last several weeks to see what needs some attention. I will fix both of the issues you raised related to the fit history in the next release, hopefully before the end of December. At the end of your email from late October, you asked a question about the evaluation of error bars. The problem with the min/max method of constraining a parameter value is that it interferes with the ability to evaluate error bars. This is pretty easy to understand. Suppose that the fit really wants the amplitude to be 0.75, but you have constrained it to be between 0.8 and 1, as shown below. As the fit progresses, it moves "amp" to smaller and smaller values. Eventually, it tries a value smaller than 0.8. Your constrained amplitude then evaluates to 0.8. If the fit tries an even smaller value, the result of the fit does not change. This is the fundamental problem with the mix/max trick. The correlations and error bars evaluate how the fit result changes as the parameters are varied from their best fit values. With your min/max constraint, the fit stops changing once the value for "amp" drops below 0.8. If the fit doesn't change as the value of "amp" changes, the uncertainties of the parameters cannot be evaluated. So does that mean the min/max trick is useless? Well, no. It tells you something about your fit. Specifically, it tells you that the value of "amp" *really* wants to be smaller than 0.8. Which is to say, you may need to revisit assumption about the appropriate value of "amp". Can you do something better than the min/max trick? Well, using Larch would help -- Larch will have much more robust support for variables with boundaries. But Artemis does not yet use Larch. Restraints help. Read the answer to the first FAQ question at http://cars9.uchicago.edu/ifeffit/FAQ/FeffitModeling In particular, check out the text attributed to Scott. Hope that helps, B On Friday, October 26, 2012 10:42:05 AM Nilmar Camilo wrote: > Another problem is related to the statistical errors when constraining the > S0^2 parameter to float between two limits. The program doesn’t return the > error for all others parameters (but just zero as the error value) as you > can see below: > > > > guess parameters: > amp= 0.79284158# +/- 0. [0.95] > enot = 5.29826510# +/- 0. [0] > delrIn11 = 0.00235278# +/- 0. [0] > ssIn11 = 0.00155959# +/- 0. [0.00300] > delrCe1= -0.00231455# +/- 0. [0] > ssCe1 = 0.00192778# +/- 0. [0.00300] > delrIn11In11 = 0.02070081# +/- 0. [0] > delrIr1= -0.00435502# +/- 0. [0] > ssIr1 = 0.00386517# +/- 0. [0.00300] > delrIn31 = 0.00648507# +/- 0. [0] > ssIn31 = 0.00669602# +/- 0. [0.00300] > delrIn12 = 0.00255704# +/- 0. [0] > ssIn12 = 0.00305432# +/- 0. [0.00300] > > def > parameters: > b = 0.8000# [min(max(0.8,amp),1.0)] > > -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage:http://xafs.org/BruceRavel Software:https://github.com/bruceravel ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Plot multiple fits in (D)Artemis and statistical errors
Hi, I am aware of both of these problems. The tool for overplotting fits from the fit history is currently broken. So is the tool for restoring an old fit. Fixing both of those is on my list of things to do. Sorry for the inconvenience. B From: ifeffit-boun...@millenia.cars.aps.anl.gov [ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Nilmar Camilo [nil...@fis.ufu.br] Sent: Friday, October 26, 2012 8:42 AM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Plot multiple fits in (D)Artemis and statistical errors Dear Bruce, I am new in the list and really don’t know if the points raised below were already discussed. In the (D)Artemis (Demeter version 0.9.13) how may I: - Plot different fits with the experimental data (to visually compare the results) - I don’t know if this is a (new) bug of the program but when I try to restore a fit the program closes. In the log file the following line is written: “Can't use an undefined value as a HASH reference at C:/Strawberry/perl/site/lib/Demeter/Fit.pm line 1558.” Obs.: I am running Demeter in Windows 7 (Pro). Another problem is related to the statistical errors when constraining the S0^2 parameter to float between two limits. The program doesn’t return the error for all others parameters (but just zero as the error value) as you can see below: guess parameters: amp= 0.79284158# +/- 0. [0.95] enot = 5.29826510# +/- 0. [0] delrIn11 = 0.00235278# +/- 0. [0] ssIn11 = 0.00155959# +/- 0. [0.00300] delrCe1= -0.00231455# +/- 0. [0] ssCe1 = 0.00192778# +/- 0. [0.00300] delrIn11In11 = 0.02070081# +/- 0. [0] delrIr1= -0.00435502# +/- 0. [0] ssIr1 = 0.00386517# +/- 0. [0.00300] delrIn31 = 0.00648507# +/- 0. [0] ssIn31 = 0.00669602# +/- 0. [0.00300] delrIn12 = 0.00255704# +/- 0. [0] ssIn12 = 0.00305432# +/- 0. [0.00300] def parameters: b = 0.8000# [min(max(0.8,amp),1.0)] Thanks so much in advance. Nilmar ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Plot multiple fits in (D)Artemis and statistical errors
Hello Nilmar, You mention floating the so2 value between two values? Can you constrain that value and completely remove it from the fit? It can usually be reasonably determined by standards. You might also take a look at the correlations in your fit. As another general guideline, when posting issues you come across, a very helpful step is to find and attach the log file in the Demeter folder after the error occurs, such as the program closing, which gives detailed information of the problem. I don't remember the exact location for the file but if you search the mailing list for the DArtemislog or artemis log file, you should be able to find it. You also have many parameters that you are fitting. Could you establish any sorts of relationships or approximations between them in order to reduce the number? You have ss for In and Ir which are quite close in value as well as delrIn11 = 0.00235278 and delrIn12 = 0.00255704# +/- 0. [0] . You could set them equal to each other and this can reduce the uncertainty of the fit. buena salud, Chris On Fri, Oct 26, 2012 at 8:42 AM, Nilmar Camilo wrote: > Dear Bruce, > > ** ** > > I am new in the list and really don’t know if the points raised below were > already discussed. > > In the (D)Artemis (Demeter version 0.9.13) how may I: > > **- **Plot different fits with the experimental data (to > visually compare the results) > > **- **I don’t know if this is a (new) bug of the program but > when I try to restore a fit the program closes. In the log file the > following line is written: “Can't use an undefined value as a HASH > reference at C:/Strawberry/perl/site/lib/Demeter/Fit.pm line 1558.” > > Obs.: I am running Demeter in Windows 7 (Pro). > > ** ** > > Another problem is related to the statistical errors when constraining the > S0^2 parameter to float between two limits. The program doesn’t return the > error for all others parameters (but just zero as the error value) as you > can see below: > > ** ** > > guess parameters: > > > amp= 0.79284158# +/- 0. [0.95] > > enot = 5.29826510# +/- 0. [0] > > delrIn11 = 0.00235278# +/- 0. [0] > > ssIn11 = 0.00155959# +/- 0. [0.00300]*** > * > > delrCe1= -0.00231455# +/- 0. [0] > > ssCe1 = 0.00192778# +/- 0. [0.00300]*** > * > > delrIn11In11 = 0.02070081# +/- 0. [0] > > delrIr1= -0.00435502# +/- 0. [0] > > ssIr1 = 0.00386517# +/- 0. [0.00300]*** > * > > delrIn31 = 0.00648507# +/- 0. [0] > > ssIn31 = 0.00669602# +/- 0. [0.00300]*** > * > > delrIn12 = 0.00255704# +/- 0. [0] > > ssIn12 = 0.00305432# +/- 0. [0.00300]*** > * > > ** ** > > def > parameters: > > > b = 0.8000# [min(max(0.8,amp),1.0)] > > ** ** > > ** ** > > Thanks so much in advance. > > Nilmar > > ** ** > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > -- Christopher J. Patridge PhD. Contact: (315)-529-0501 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] Plot multiple fits in (D)Artemis and statistical errors
Dear Bruce, I am new in the list and really don't know if the points raised below were already discussed. In the (D)Artemis (Demeter version 0.9.13) how may I: - Plot different fits with the experimental data (to visually compare the results) - I don't know if this is a (new) bug of the program but when I try to restore a fit the program closes. In the log file the following line is written: "Can't use an undefined value as a HASH reference at C:/Strawberry/perl/site/lib/Demeter/Fit.pm line 1558." Obs.: I am running Demeter in Windows 7 (Pro). Another problem is related to the statistical errors when constraining the S0^2 parameter to float between two limits. The program doesn't return the error for all others parameters (but just zero as the error value) as you can see below: guess parameters: amp= 0.79284158# +/- 0. [0.95] enot = 5.29826510# +/- 0. [0] delrIn11 = 0.00235278# +/- 0. [0] ssIn11 = 0.00155959# +/- 0. [0.00300] delrCe1= -0.00231455# +/- 0. [0] ssCe1 = 0.00192778# +/- 0. [0.00300] delrIn11In11 = 0.02070081# +/- 0. [0] delrIr1= -0.00435502# +/- 0. [0] ssIr1 = 0.00386517# +/- 0. [0.00300] delrIn31 = 0.00648507# +/- 0. [0] ssIn31 = 0.00669602# +/- 0. [0.00300] delrIn12 = 0.00255704# +/- 0. [0] ssIn12 = 0.00305432# +/- 0. [0.00300] def parameters: b = 0.8000# [min(max(0.8,amp),1.0)] Thanks so much in advance. Nilmar ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
