Re: [Ifeffit] fitting a specific k range
Matt, At the risk of coming off sounding a bit mean, I don't think you are asking a very well-posed question. Examining the history of this project, I see that you are fitting in q space. Like Matt, this is not my favorite choice, but there is nothing horribly wrong about it, so long as you understand what you are doing. What is problematic is your expectation that, in doing so, you should be better able to fit a particular feature in k space. If you examine the data in k and q space, you will see that the act of Fourier filtering the data (i.e. plotting in q space) has the effect of suppressing the wiggle at 5 inv. Ang. that you are asking about. Given that you are fitting in q-space, it is completely unreasonable (from a numerical perspective) to expect that the fit could possibly reproduce a feature that you have (intentionally or otherwise) filtered out of the data. To say that another way, given how you constructed the fit, you got a good fit. You made the fit in a way that it cannot possibly reproduce the feature you are asking about, thus your question is ill-posed. I think the deeper problem is that you don't have a deep grasp of what happens in Fourier analysis. So let's talk about that a bit. When you do the transform from k to R-space, you are representing the frequency spectrum contained in the original data. Slow wiggling features in the original data give rise to the low-R (i.e. low-frequency) features in the chi(R) data. Fast wiggling features in chi(k) give rise to high-R features in chi(R). Your wiggle at 5 inv. Ang. looks to my eye like a pretty high frequency feature. When you do the backwards transform from k to R with a restricted R range (in your case, from 1 to 3.5), you are filtering frequencies out of the data. The chi(q) data only contains those frequencies from the original chi(k) spectrum that fall in your R range. What I am suggesting is that the wiggle in question is due to Fourier components beyond 3.5 Ang in chi(R). So, how would you reproduce that feature in chi(k)? That's simple -- fit features in the data beyond 3.5 in chi(R). That is, do an actual good job of fitting the small signal from 3.5 to 5 Ang in R. Of course, that's going to be difficult to do in a statistically robust manner because the signal is very small, there will be quite a large number of paths contributing to that region, and the parameterization of many paths for such a small signal is likely not to be very robust. EXAFS is hard! Hope that helps, B On 12/04/2013 02:17 PM, Matt Frith wrote: Dear All, I need some help in fitting an amorphous iron oxyhydoxide sample. I am having difficulty producing a good fit, particularly in the k=4-6 range. Fitting this region well is very important for me, because if I add another metal(+3 oxidation state) into my system, this is where I observe the most quantifiable changes (The shoulder @ 5 A^-1 and the min @ 5.6 A^-1). Thus far I have been unable to fit the shoulder well enough to make meaningful comparisons. I have been fitting in kq with kmin=2.566 And kmax=10.877, and Rmin=1 and Rmax=3.5, and using the goethite O1.1, Fe.1, and Fe.3 paths. Attached is an Artemis file (P41_006_merge_norm_TRANS.fpj) for an amorphous Fe oxyhydroxide sample (Fe only, no other metals). The data was collected at the Fe K-edge. *Is there a way to fit just this region (k~4-6 range) in k? If so what is the best method for doing this? If not, does anyone have suggestions as to how I can improve my fitting? Should I fit the data in k since the shoulder is less evident in kq?* Thank you for your time. Sincerely, Matt Frith ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science 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] fitting a specific k range
Matt, Outside of the question of fitting the data, can you collect absorption data on the additional 3+ metal you are adding the material? Chris *** Dr. Christopher Patridge Assistant Professor Department of Math and Natural Sciences D'youville College Contact: 315-529-0501 On Dec 5, 2013, at 10:11 AM, Bruce Ravel bra...@bnl.gov wrote: Matt, At the risk of coming off sounding a bit mean, I don't think you are asking a very well-posed question. Examining the history of this project, I see that you are fitting in q space. Like Matt, this is not my favorite choice, but there is nothing horribly wrong about it, so long as you understand what you are doing. What is problematic is your expectation that, in doing so, you should be better able to fit a particular feature in k space. If you examine the data in k and q space, you will see that the act of Fourier filtering the data (i.e. plotting in q space) has the effect of suppressing the wiggle at 5 inv. Ang. that you are asking about. Given that you are fitting in q-space, it is completely unreasonable (from a numerical perspective) to expect that the fit could possibly reproduce a feature that you have (intentionally or otherwise) filtered out of the data. To say that another way, given how you constructed the fit, you got a good fit. You made the fit in a way that it cannot possibly reproduce the feature you are asking about, thus your question is ill-posed. I think the deeper problem is that you don't have a deep grasp of what happens in Fourier analysis. So let's talk about that a bit. When you do the transform from k to R-space, you are representing the frequency spectrum contained in the original data. Slow wiggling features in the original data give rise to the low-R (i.e. low-frequency) features in the chi(R) data. Fast wiggling features in chi(k) give rise to high-R features in chi(R). Your wiggle at 5 inv. Ang. looks to my eye like a pretty high frequency feature. When you do the backwards transform from k to R with a restricted R range (in your case, from 1 to 3.5), you are filtering frequencies out of the data. The chi(q) data only contains those frequencies from the original chi(k) spectrum that fall in your R range. What I am suggesting is that the wiggle in question is due to Fourier components beyond 3.5 Ang in chi(R). So, how would you reproduce that feature in chi(k)? That's simple -- fit features in the data beyond 3.5 in chi(R). That is, do an actual good job of fitting the small signal from 3.5 to 5 Ang in R. Of course, that's going to be difficult to do in a statistically robust manner because the signal is very small, there will be quite a large number of paths contributing to that region, and the parameterization of many paths for such a small signal is likely not to be very robust. EXAFS is hard! Hope that helps, B On 12/04/2013 02:17 PM, Matt Frith wrote: Dear All, I need some help in fitting an amorphous iron oxyhydoxide sample. I am having difficulty producing a good fit, particularly in the k=4-6 range. Fitting this region well is very important for me, because if I add another metal(+3 oxidation state) into my system, this is where I observe the most quantifiable changes (The shoulder @ 5 A^-1 and the min @ 5.6 A^-1). Thus far I have been unable to fit the shoulder well enough to make meaningful comparisons. I have been fitting in kq with kmin=2.566 And kmax=10.877, and Rmin=1 and Rmax=3.5, and using the goethite O1.1, Fe.1, and Fe.3 paths. Attached is an Artemis file (P41_006_merge_norm_TRANS.fpj) for an amorphous Fe oxyhydroxide sample (Fe only, no other metals). The data was collected at the Fe K-edge. *Is there a way to fit just this region (k~4-6 range) in k? If so what is the best method for doing this? If not, does anyone have suggestions as to how I can improve my fitting? Should I fit the data in k since the shoulder is less evident in kq?* Thank you for your time. Sincerely, Matt Frith ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science 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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] fitting a specific k range
First, a disclaimer--I haven't looked at the data Matt sent (it's a busy time of year!), but I disagree in a general sense with my reading of what Bruce wrote (perhaps I am reading it wrong). In particular, I disagree with this statement: Given that you are fitting in q-space, it is completely unreasonable (from a numerical perspective) to expect that the fit could possibly reproduce a feature that you have (intentionally or otherwise) filtered out of the data. To say that another way, given how you constructed the fit, you got a good fit. You made the fit in a way that it cannot possibly reproduce the feature you are asking about, thus your question is ill-posed. To explain why, suppose I am fitting a standard--for the sake of a simple example, suppose it's copper. I include in my model paths out to 7 angstroms, including multiple-scattering paths, and use a Debye model for the MSRDs. It's possible to do a pretty good job in that kind of fit with just a few free parameters: S02, E0, an isotropic lattice expansion, and a Debye temperature. Now, suppose I perform the fit from 1 to 3.5 angstroms. Usually, the fit will do a pretty good job reproducing features well above 3.5 angstroms, because they're in the model (the paths are included) even though they're not in the fitting range. That's true for features in k-space that are caused by high-R paths too, of course. In fact, that kind of fit is particularly valuable to me, because it strongly suggests I've got the model right--I've essentially hid the high-R data from the numerical routines, so if it fits that region well anyway, it's probably because the model itself is a good one. While I defend that principle as a very important one, I'm not claiming it applies in Matt's case--it probably doesn't. To reproduce features at high-R, it IS necessary to have a model (i.e. paths) that cover the high-R contribution, and it sounds like Matt does not have those paths included in his model. But it's not necessary to FIT up to high R. --Scott Calvin Sarah Lawrence College P.S. My least favorite warning that Artemis provides is the one that tells you that you're including paths outside the fitting region, for just this reason. It's easy enough to change the preferences so that Artemis doesn't give that warning, and it's usually one of the first things I have my students do when they're first learning to fit. On Dec 5, 2013, at 10:11 AM, Bruce Ravel bra...@bnl.gov wrote: Matt, At the risk of coming off sounding a bit mean, I don't think you are asking a very well-posed question. Examining the history of this project, I see that you are fitting in q space. Like Matt, this is not my favorite choice, but there is nothing horribly wrong about it, so long as you understand what you are doing. What is problematic is your expectation that, in doing so, you should be better able to fit a particular feature in k space. If you examine the data in k and q space, you will see that the act of Fourier filtering the data (i.e. plotting in q space) has the effect of suppressing the wiggle at 5 inv. Ang. that you are asking about. Given that you are fitting in q-space, it is completely unreasonable (from a numerical perspective) to expect that the fit could possibly reproduce a feature that you have (intentionally or otherwise) filtered out of the data. To say that another way, given how you constructed the fit, you got a good fit. You made the fit in a way that it cannot possibly reproduce the feature you are asking about, thus your question is ill-posed. I think the deeper problem is that you don't have a deep grasp of what happens in Fourier analysis. So let's talk about that a bit. When you do the transform from k to R-space, you are representing the frequency spectrum contained in the original data. Slow wiggling features in the original data give rise to the low-R (i.e. low-frequency) features in the chi(R) data. Fast wiggling features in chi(k) give rise to high-R features in chi(R). Your wiggle at 5 inv. Ang. looks to my eye like a pretty high frequency feature. When you do the backwards transform from k to R with a restricted R range (in your case, from 1 to 3.5), you are filtering frequencies out of the data. The chi(q) data only contains those frequencies from the original chi(k) spectrum that fall in your R range. What I am suggesting is that the wiggle in question is due to Fourier components beyond 3.5 Ang in chi(R). So, how would you reproduce that feature in chi(k)? That's simple -- fit features in the data beyond 3.5 in chi(R). That is, do an actual good job of fitting the small signal from 3.5 to 5 Ang in R. Of course, that's going to be difficult to do in a statistically robust manner because the signal is very small, there will be quite a large number of paths contributing to that region, and the parameterization of many paths for such a small signal
Re: [Ifeffit] fitting a specific k range
On 12/05/2013 12:18 PM, Scott Calvin wrote: While I defend that principle as a very important one, I'm not claiming it applies in Matt's case--it probably doesn't. To reproduce features at high-R, it IS necessary to have a model (i.e. paths) that cover the high-R contribution, and it sounds like Matt does not have those paths included in his model. But it's not necessary to FIT up to high R. It doesn't apply. Matt filtered his data. Matt used paths that only include Fourier components within the filtered band. To suggest that it may somehow be reasonable that the fit could turn out other than how it did runs a real risk of misleading this fellow who is, apparently, a newcomer to EXAFS analysis. P.S. My least favorite warning that Artemis provides is the one that tells you that you're including paths outside the fitting region, for just this reason. It's easy enough to change the preferences so that Artemis doesn't give that warning, and it's usually one of the first things I have my students do when they're first learning to fit. OK. Whatever. Instead of complaining about this, perhaps you should consider hosannas of gratitude that I make it possible, easy even, to accommodate preferences different from my own. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science 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] fitting a specific k range
Bruce, Without those friendly warnings (reminders), beginners would likely fall down several rabbit holes before understanding many of the important steps necessary to get meaningful answers in EXAFS. I know I would have. Chris *** Dr. Christopher Patridge Assistant Professor Department of Math and Natural Sciences D'youville College Contact: 315-529-0501 On Dec 5, 2013, at 1:19 PM, Bruce Ravel bra...@bnl.gov wrote: On 12/05/2013 12:18 PM, Scott Calvin wrote: While I defend that principle as a very important one, I'm not claiming it applies in Matt's case--it probably doesn't. To reproduce features at high-R, it IS necessary to have a model (i.e. paths) that cover the high-R contribution, and it sounds like Matt does not have those paths included in his model. But it's not necessary to FIT up to high R. It doesn't apply. Matt filtered his data. Matt used paths that only include Fourier components within the filtered band. To suggest that it may somehow be reasonable that the fit could turn out other than how it did runs a real risk of misleading this fellow who is, apparently, a newcomer to EXAFS analysis. P.S. My least favorite warning that Artemis provides is the one that tells you that you're including paths outside the fitting region, for just this reason. It's easy enough to change the preferences so that Artemis doesn't give that warning, and it's usually one of the first things I have my students do when they're first learning to fit. OK. Whatever. Instead of complaining about this, perhaps you should consider hosannas of gratitude that I make it possible, easy even, to accommodate preferences different from my own. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science 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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] fitting a specific k range
Besides, that's a (very common) misuse of the word hosanna. -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Anatoly I Frenkel Sent: Thursday, December 05, 2013 12:29 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] fitting a specific k range I object the use of hosannas of adoration. Other than the use of Greek mythology, I propose the mailing list to be religion-neutral and tautology-free. How about you should consider praise or adoration, instead of you should consider hosannas of gratitude. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov [ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Bruce Ravel [bra...@bnl.gov] Sent: Thursday, December 05, 2013 1:19 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] fitting a specific k range On 12/05/2013 12:18 PM, Scott Calvin wrote: While I defend that principle as a very important one, I'm not claiming it applies in Matt's case--it probably doesn't. To reproduce features at high-R, it IS necessary to have a model (i.e. paths) that cover the high-R contribution, and it sounds like Matt does not have those paths included in his model. But it's not necessary to FIT up to high R. It doesn't apply. Matt filtered his data. Matt used paths that only include Fourier components within the filtered band. To suggest that it may somehow be reasonable that the fit could turn out other than how it did runs a real risk of misleading this fellow who is, apparently, a newcomer to EXAFS analysis. P.S. My least favorite warning that Artemis provides is the one that tells you that you're including paths outside the fitting region, for just this reason. It's easy enough to change the preferences so that Artemis doesn't give that warning, and it's usually one of the first things I have my students do when they're first learning to fit. OK. Whatever. Instead of complaining about this, perhaps you should consider hosannas of gratitude that I make it possible, easy even, to accommodate preferences different from my own. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science 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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] fitting a specific k range
I object the use of hosannas of adoration. Other than the use of Greek mythology, I propose the mailing list to be religion-neutral and tautology-free. How about you should consider praise or adoration, instead of you should consider hosannas of gratitude. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov [ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Bruce Ravel [bra...@bnl.gov] Sent: Thursday, December 05, 2013 1:19 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] fitting a specific k range On 12/05/2013 12:18 PM, Scott Calvin wrote: While I defend that principle as a very important one, I'm not claiming it applies in Matt's case--it probably doesn't. To reproduce features at high-R, it IS necessary to have a model (i.e. paths) that cover the high-R contribution, and it sounds like Matt does not have those paths included in his model. But it's not necessary to FIT up to high R. It doesn't apply. Matt filtered his data. Matt used paths that only include Fourier components within the filtered band. To suggest that it may somehow be reasonable that the fit could turn out other than how it did runs a real risk of misleading this fellow who is, apparently, a newcomer to EXAFS analysis. P.S. My least favorite warning that Artemis provides is the one that tells you that you're including paths outside the fitting region, for just this reason. It's easy enough to change the preferences so that Artemis doesn't give that warning, and it's usually one of the first things I have my students do when they're first learning to fit. OK. Whatever. Instead of complaining about this, perhaps you should consider hosannas of gratitude that I make it possible, easy even, to accommodate preferences different from my own. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science 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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] fitting a specific k range
Scott, On Thu, Dec 5, 2013 at 11:18 AM, Scott Calvin scal...@sarahlawrence.edu wrote: First, a disclaimer--I haven't looked at the data Matt sent (it's a busy time of year!), but I disagree in a general sense with my reading of what Bruce wrote (perhaps I am reading it wrong). In particular, I disagree with this statement: Given that you are fitting in q-space, it is completely unreasonable (from a numerical perspective) to expect that the fit could possibly reproduce a feature that you have (intentionally or otherwise) filtered out of the data. To say that another way, given how you constructed the fit, you got a good fit. You made the fit in a way that it cannot possibly reproduce the feature you are asking about, thus your question is ill-posed. To explain why, suppose I am fitting a standard--for the sake of a simple example, suppose it's copper. I include in my model paths out to 7 angstroms, including multiple-scattering paths, and use a Debye model for the MSRDs. It's possible to do a pretty good job in that kind of fit with just a few free parameters: S02, E0, an isotropic lattice expansion, and a Debye temperature. Now, suppose I perform the fit from 1 to 3.5 angstroms. Usually, the fit will do a pretty good job reproducing features well above 3.5 angstroms, because they're in the model (the paths are included) even though they're not in the fitting range. That's true for features in k-space that are caused by high-R paths too, of course. In fact, that kind of fit is particularly valuable to me, because it strongly suggests I've got the model right--I've essentially hid the high-R data from the numerical routines, so if it fits that region well anyway, it's probably because the model itself is a good one. While I defend that principle as a very important one, I'm not claiming it applies in Matt's case--it probably doesn't. To reproduce features at high-R, it IS necessary to have a model (i.e. paths) that cover the high-R contribution, and it sounds like Matt does not have those paths included in his model. But it's not necessary to FIT up to high R. I agree that if a model fitted to data over some limited range of data (either k or R, or even some external variable) matches data well outside that range, that is a good feature of the model. But what if it doesn't match the data outside that range? As you say, model that matches data over a very limited range can be useful, but mostly in the context for how it extrapolates outside that range. Back to Matt's point: using a sharp feature in chi(k) can be a reasonable spectroscopic approach to identifying particular phases of materials (mineral phases for example).But to actually model any of these sharp features in chi(k) would require a large R range for the data, and might require many paths. Trying to model such a limited range while ignoring data outside that range is not a good idea. P.S. My least favorite warning that Artemis provides is the one that tells you that you're including paths outside the fitting region, for just this reason. It's easy enough to change the preferences so that Artemis doesn't give that warning, and it's usually one of the first things I have my students do when they're first learning to fit. When teaching students to drive a car is showing them how to put a piece of electrical tape over the Check Engine light the first thing you do? Generally, false positives warnings are preferable to having no warnings. --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] fitting a specific k range
What I find reassuring about Bruce's warnings is they allow you to think properly about what you are doing. Fortunately, unlike Chris, I am not of a size where I have to worry about falling down rabbit holes, unless American rabbits are much bigger than English ones. I would commend Matt's original question as it opened a debate with 3 of the mainstays of the list. That may not have been the intention but it makes interesting reading for us mailing list voyeurs. Cheers Fred Sent from Samsung tablet ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] fitting a specific k range
Hi Anatoly, On Thu, Dec 5, 2013 at 12:28 PM, Anatoly I Frenkel afren...@yu.edu wrote: I object the use of hosannas of adoration. Other than the use of Greek mythology, I propose the mailing list to be religion-neutral and tautology-free. Is Down the rabbit hole OK? I'm not sure it usually counts as a religious text to you, but I'm rather fond of Alice's Adventures and find it to many useful words to live by. I don't read it as being True (in the religious sense that De Rerum Natura,The Odyssey, Don Quixote, Moby Dick, The Lord of the Rings, and the works of Jorge Luis Borges and Bob Dylan are), but it does seem somewhat more realistic and useful than some of those other standard texts from antiquity. That could just be me. I certainly mean no offense to anyone's belief system ;) --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] fitting a specific k range
It must be a slow day in the EXAFS world. Does the term 'topic drift' mean anything? :-) The Wikipedia entry http://en.wikipedia.org/wiki/Hosanna has some examples of secular use of the word, FWIW, which I admit isn't much. mam On 12/5/2013 2:02 PM, Matt Newville wrote: Hi Anatoly, On Thu, Dec 5, 2013 at 12:28 PM, Anatoly I Frenkel afren...@yu.edu wrote: I object the use of hosannas of adoration. Other than the use of Greek mythology, I propose the mailing list to be religion-neutral and tautology-free. Is Down the rabbit hole OK? I'm not sure it usually counts as a religious text to you, but I'm rather fond of Alice's Adventures and find it to many useful words to live by. I don't read it as being True (in the religious sense that De Rerum Natura,The Odyssey, Don Quixote, Moby Dick, The Lord of the Rings, and the works of Jorge Luis Borges and Bob Dylan are), but it does seem somewhat more realistic and useful than some of those other standard texts from antiquity. That could just be me. I certainly mean no offense to anyone's belief system ;) --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] fitting a specific k range
I love the warnings Artemis gives! They're not just for novices--they often catch when I've made a dumb mistake somewhere. I praise them, defend them, and generally think Bruce has done a wonderful thing by having them. The out of range default warning, however, I find counterproductive and confusing to novices. There are two reasons for my opinion (and it is, of course, my opinion--as Bruce points out, if others differ, they can set the defaults differently.) One has to do with the kind of example I mentioned earlier. Here's the other reason: The default behavior is to warn if there is a path beyond 1.1 times the top of the range, correct? (It's kind of a pain for me right now to fire up the most recent version of Artemis, so I can't actually easily confirm that at the moment.) The default R-max is, if I recall correctly, 3.0 angstroms. Thus, by default, a warning is generated if there is a path above 3.3 angstroms in the list. But, as we know, the path list uses distances which are half path lengths, while the Fourier transform range is in terms of the conjugate variable to k. For edges around the third row of the periodic table, the peaks corresponding to a path tend to show up about 0.3 to 0.5 angstroms lower in the Fourier transform than their half path-length. And, of course, that's just the peak--the path has significant amplitude a bit below (and above) that. So, a novice user fires up Artemis, imports her data, and uses atoms to generate a feff file. Because she's appropriately thoughtful about what she's doing, she looks at what the unfitted paths of the FEFF calculation look like. She sees the fitting range goes up to 3 angstroms, and then selects all the paths that contribute significant amplitude to that range. That might include a path with a half path length of 3.4 angstroms. She then runs a fit--and Artemis gives her a warning that something may be wrong. At that point, she could stick to her guns and tell the fit to continue. Since that's going to happen with pretty much every fit she runs, it becomes very tempting not to read the warning each time, but just dismiss it. And at that point, if there's a highly useful warning, she'll miss it. Or, she could decide that she's the novice, and what she's doing isn't that unusual, so maybe she shouldn't be including that path at 3.4 angstroms, and take it out. She is now getting distorted results, because she's leaving out a path that has significant amplitude in the region. I think, not just from personal preference, but also from a consideration of what is best for people learning to use the software, that the warning is set too conservatively. And I'm not even clear what misstep it's trying to prevent. --Scott Calvin Sarah Lawrence College On Dec 5, 2013, at 2:32 PM, fred.mosselm...@diamond.ac.uk fred.mosselm...@diamond.ac.uk wrote: What I find reassuring about Bruce's warnings is they allow you to think properly about what you are doing. Fortunately, unlike Chris, I am not of a size where I have to worry about falling down rabbit holes, unless American rabbits are much bigger than English ones. I would commend Matt's original question as it opened a debate with 3 of the mainstays of the list. That may not have been the intention but it makes interesting reading for us mailing list voyeurs. Cheers Fred Sent from Samsung tablet ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] fitting a specific k range
Hi Scott, On Thu, Dec 5, 2013 at 4:56 PM, Scott Calvin scal...@sarahlawrence.edu wrote: I love the warnings Artemis gives! They're not just for novices--they often catch when I've made a dumb mistake somewhere. I praise them, defend them, and generally think Bruce has done a wonderful thing by having them. The out of range default warning, however, I find counterproductive and confusing to novices. There are two reasons for my opinion (and it is, of course, my opinion--as Bruce points out, if others differ, they can set the defaults differently.) One has to do with the kind of example I mentioned earlier. Here's the other reason: The default behavior is to warn if there is a path beyond 1.1 times the top of the range, correct? (It's kind of a pain for me right now to fire up the most recent version of Artemis, so I can't actually easily confirm that at the moment.) The default R-max is, if I recall correctly, 3.0 angstroms. Thus, by default, a warning is generated if there is a path above 3.3 angstroms in the list. But, as we know, the path list uses distances which are half path lengths, while the Fourier transform range is in terms of the conjugate variable to k. For edges around the third row of the periodic table, the peaks corresponding to a path tend to show up about 0.3 to 0.5 angstroms lower in the Fourier transform than their half path-length. And, of course, that's just the peak--the path has significant amplitude a bit below (and above) that. So, a novice user fires up Artemis, imports her data, and uses atoms to generate a feff file. Because she's appropriately thoughtful about what she's doing, she looks at what the unfitted paths of the FEFF calculation look like. She sees the fitting range goes up to 3 angstroms, and then selects all the paths that contribute significant amplitude to that range. That might include a path with a half path length of 3.4 angstroms. She then runs a fit--and Artemis gives her a warning that something may be wrong. At that point, she could stick to her guns and tell the fit to continue. Since that's going to happen with pretty much every fit she runs, it becomes very tempting not to read the warning each time, but just dismiss it. And at that point, if there's a highly useful warning, she'll miss it. Or, she could decide that she's the novice, and what she's doing isn't that unusual, so maybe she shouldn't be including that path at 3.4 angstroms, and take it out. She is now getting distorted results, because she's leaving out a path that has significant amplitude in the region. It's reasonable to question whether the threshold for such a warning is too conservative or to suggest (better yet, issue a pull request for) a fix for a particular feature. Saying (as you did) that turning the warning off usually one of the first things you teach students seems counterproductive. To be clear, you did not teach them to change the default value of reff_margin. I would have said Mend it, don't End it. Perhaps the rule should be (Reff+0.5)*1.1? But this was not your suggestion. Your suggestion was to ignore the rule. If you are relying on these codes for your work, and teaching others to use them, and find things you don't like or could be improved, it is your responsibility to provide constructive, specific feedback and fixes to the actual code. Yes, I actually do mean you, Scott. This would be the perfect place for you to contribute. See https://github.com/bruceravel/demeter/blob/master/lib/Demeter/Fit/Sanity.pm https://github.com/bruceravel/demeter/blob/master/lib/Demeter/configuration/warnings.demeter_conf I think, not just from personal preference, but also from a consideration of what is best for people learning to use the software, that the warning is set too conservatively. And I'm not even clear what misstep it's trying to prevent. I cannot tell if you are joking. It is, of course, to prevent one from including paths (say, the second and third shells with variable parameters when the R range being fit (say the first shell) will not allow those variables to alter the fit. Having such variables can grossly distort the fit and will generally prevent good error bars from being calculated. I agree that it's not so much the presence of Paths well beyond Rmax as it is the presence of variables that only affect Paths outside the fitting range. But that is much harder to automatically detect, and the case described above is a likely way to get into that situation. Having a warning about this is vastly preferable to not having such a warning. The details of the thresholds may be tweaked, but you didn't complain about the details of the rules, but the existence of the rule itself. Perhaps your view is that this rule is just always wrong and not worth fixing, but I think many of us would disagree with you. --Matt ___ Ifeffit
