running ifeffit under 64-bit windows7
Hi, I have used ARTEMIS to fit the EXAFS of a simple Cu 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 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 can I interpret it? regards Sameh ============================================================ 32bit windows 7 Independent points = 12.172851562 Number of variables = 6.000000000 Chi-square = 53.001967099 Reduced Chi-square = 8.586301900 R-factor = 0.000163791 !!! Measurement uncertainty (k) = 0.000110566 Measurement uncertainty (R) = 0.057163282 Number of data sets = 1.000000000 Guess parameters +/- uncertainties (initial guess): amp = 0.9907500 +/- 0.0312520 (1.0000) enot = 5.6814210 +/- 0.3815760 (0.0000) delr1 = 0.0016460 +/- 0.0033990 (0.0000) ss1 = 0.0099820 +/- 0.0004090 (0.0030) w1 3rd cumulant = 0.0001710 +/- 0.0000340 (0.0000) p1 4th cumulant = 0.0000240 +/- 0.0000070 (0.0000) ============================================================ 64bit windows 7 Independent points = 12.172851562 Number of variables = 6.000000000 Chi-square = 54.036163164 Reduced Chi-square = 8.753841335 R-factor = 0.309664502E-06 !!! Measurement uncertainty (k) = 0.000097377 Measurement uncertainty (R) = 0.050344538 Number of data sets = 1.000000000 Guess parameters +/- uncertainties (initial guess): amp = 1.0029100 +/- 0.0296670 (1.0000) enot = 5.7522760 +/- 0.4614510 (0.0000) delr1 = 0.0024980 +/- 0.0040190 (0.0000) ss1 = 0.0101430 +/- 0.0003790 (0.0030) w1 3rd cumulant = 0.0001780 +/- 0.0000410 (0.0000) p1 4th cumulant = 0.0000260 +/- 0.0000070 (0.0000) ============================================================
Hi, maybe these below clarify a little bit the problem, but the problem sounds very intriguing http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2004-July/005729.html http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2005-October/006613.html http://cars9.uchicago.edu/ifeffit/FAQ/FeffitModeling I am waiting also for the answer from authors Do you see changes in the fit in R or/and K space, between systems? I suppose that all input parameters were identical... regards kicaj W dniu 12-03-10 15:17, Sameh Ibrahim Ahmed pisze:
Hi, I have used ARTEMIS to fit the EXAFS of a simple Cu 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 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 can I interpret it? regards Sameh ============================================================ 32bit windows 7 Independent points = 12.172851562 Number of variables = 6.000000000 Chi-square = 53.001967099 Reduced Chi-square = 8.586301900 R-factor = 0.000163791 !!! Measurement uncertainty (k) = 0.000110566 Measurement uncertainty (R) = 0.057163282 Number of data sets = 1.000000000
Guess parameters +/- uncertainties (initial guess): amp = 0.9907500 +/- 0.0312520 (1.0000) enot = 5.6814210 +/- 0.3815760 (0.0000) delr1 = 0.0016460 +/- 0.0033990 (0.0000) ss1 = 0.0099820 +/- 0.0004090 (0.0030) w1 3rd cumulant = 0.0001710 +/- 0.0000340 (0.0000) p1 4th cumulant = 0.0000240 +/- 0.0000070 (0.0000)
============================================================ 64bit windows 7 Independent points = 12.172851562 Number of variables = 6.000000000 Chi-square = 54.036163164 Reduced Chi-square = 8.753841335 R-factor = 0.309664502E-06 !!! Measurement uncertainty (k) = 0.000097377 Measurement uncertainty (R) = 0.050344538 Number of data sets = 1.000000000
Guess parameters +/- uncertainties (initial guess): amp = 1.0029100 +/- 0.0296670 (1.0000) enot = 5.7522760 +/- 0.4614510 (0.0000) delr1 = 0.0024980 +/- 0.0040190 (0.0000) ss1 = 0.0101430 +/- 0.0003790 (0.0030) w1 3rd cumulant = 0.0001780 +/- 0.0000410 (0.0000) p1 4th cumulant = 0.0000260 +/- 0.0000070 (0.0000) ============================================================
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Hi Kicaj,
2012/3/10 "Dr. Dariusz A. Zając"
Hi, maybe these below clarify a little bit the problem, but the problem sounds very intriguing http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2004-July/005729.html http://millenia.cars.aps.anl.gov/pipermail/ifeffit/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, reduced chi-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, you will see it stated that this should be approximately the number of degrees of freedom in the fit. Reduced chi-square is then defined to be chi-squared / (the number of degrees of freedom in the fit), so that it should be 1 (according to statistics 101). This presupposes a couple of things that aren't very true for us: a) it assumes we actually know the uncertainty in the data -- the automated estimate in ifefit is pretty simplistic. b) it assumes 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 >> 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 of the scale of the data (and so also independent of data k-range and k-weight for fits in R-space), and can more easily be made into a "rule of thumb", say "If R-factor > 0.05, then you should be wary of the results". Hope that helps, --Matt
Dear Matt, when I was answering I didnt received your answer... waiting for the answer from authors means that I suspect perhaps a problem with distribution version, what you already suggested... sorry for the confussion by my email... cheers darek/kicaj W dniu 12-03-10 17:16, Matt Newville pisze:
Hi Kicaj,
2012/3/10 "Dr. Dariusz A. Zając"
: Hi, maybe these below clarify a little bit the problem, but the problem sounds very intriguing http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2004-July/005729.html http://millenia.cars.aps.anl.gov/pipermail/ifeffit/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, reduced chi-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, you will see it stated that this should be approximately the number of degrees of freedom in the fit. Reduced chi-square is then defined to be chi-squared / (the number of degrees of freedom in the fit), so that it should be 1 (according to statistics 101). This presupposes a couple of things that aren't very true for us: a) it assumes we actually know the uncertainty in the data -- the automated estimate in ifefit is pretty simplistic. b) it assumes 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>> 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 of the scale of the data (and so also independent of data k-range and k-weight for fits in R-space), and can more easily be made into a "rule of thumb", say "If R-factor> 0.05, then you should be wary of the results".
Hope that helps,
--Matt
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Hi Kicaj,
OK, sorry I misunderstood then. And, despite my laziness, I think
that Sameh is right that it's probably time for a more complete
update.... Such a thing should probably feature Bruce's newer codes of
course.
--Matt
On Sat, Mar 10, 2012 at 10:16 AM, Matt Newville
Hi Kicaj,
2012/3/10 "Dr. Dariusz A. Zając"
: Hi, maybe these below clarify a little bit the problem, but the problem sounds very intriguing http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2004-July/005729.html http://millenia.cars.aps.anl.gov/pipermail/ifeffit/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, reduced chi-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, you will see it stated that this should be approximately the number of degrees of freedom in the fit. Reduced chi-square is then defined to be chi-squared / (the number of degrees of freedom in the fit), so that it should be 1 (according to statistics 101). This presupposes a couple of things that aren't very true for us: a) it assumes we actually know the uncertainty in the data -- the automated estimate in ifefit is pretty simplistic. b) it assumes 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 >> 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 of the scale of the data (and so also independent of data k-range and k-weight for fits in R-space), and can more easily be made into a "rule of thumb", say "If R-factor > 0.05, then you should be wary of the results".
Hope that helps,
--Matt
-- --Matt Newville <newville at cars.uchicago.edu> 630-252-0431
Hi Sameh,
On Sat, Mar 10, 2012 at 8:17 AM, Sameh Ibrahim Ahmed
Hi,
I have used ARTEMIS to fit the EXAFS of a simple Cu 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 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 can I interpret it?
regards Sameh
============================================================ 32bit windows 7 Independent points = 12.172851562 Number of variables = 6.000000000 Chi-square = 53.001967099 Reduced Chi-square = 8.586301900 R-factor = 0.000163791 !!! Measurement uncertainty (k) = 0.000110566 Measurement uncertainty (R) = 0.057163282 Number of data sets = 1.000000000
Guess parameters +/- uncertainties (initial guess): amp = 0.9907500 +/- 0.0312520 (1.0000) enot = 5.6814210 +/- 0.3815760 (0.0000) delr1 = 0.0016460 +/- 0.0033990 (0.0000) ss1 = 0.0099820 +/- 0.0004090 (0.0030) w1 3rd cumulant = 0.0001710 +/- 0.0000340 (0.0000) p1 4th cumulant = 0.0000240 +/- 0.0000070 (0.0000)
============================================================ 64bit windows 7 Independent points = 12.172851562 Number of variables = 6.000000000 Chi-square = 54.036163164 Reduced Chi-square = 8.753841335 R-factor = 0.309664502E-06 !!! Measurement uncertainty (k) = 0.000097377 Measurement uncertainty (R) = 0.050344538 Number of data sets = 1.000000000
Guess parameters +/- uncertainties (initial guess): amp = 1.0029100 +/- 0.0296670 (1.0000) enot = 5.7522760 +/- 0.4614510 (0.0000) delr1 = 0.0024980 +/- 0.0040190 (0.0000) ss1 = 0.0101430 +/- 0.0003790 (0.0030) w1 3rd cumulant = 0.0001780 +/- 0.0000410 (0.0000) p1 4th cumulant = 0.0000260 +/- 0.0000070 (0.0000) ============================================================
Except for R-factor, these differences are pretty small -- all parameters are well within the estimated error bars. I'm not sure why R-factor is different. I would say that there is essentially no difference in what to report.... the R factors are both small enough to mean "very good fit", and any difference between them would really only important when comparing two different fits -- in that case, just be consistent. But that's not to say that it's not worth trying to understand the difference.... but that might take a bit of investigative work. One thing I noticed in the projects you sent (only to me -- please use the mailing list!!) is that these fits use different versions of Athena and ifeffit: 32bit Win7: Artemis 0.8.012, ifeffit 1.2.11 64bin Win7: Artemis 0.8.014, ifeffit 1.2.11c Off hand, I don't know that either of these is actually significant. --Matt
participants (3)
-
"Dr. Dariusz A. Zając"
-
Matt Newville
-
Sameh Ibrahim Ahmed