March 2004 - Ifeffit - millenia.cars.aps.anl.gov

small update, unix only
by Bruce Ravel 10 Mar '04

10 Mar '04

Hi folks, I corrected a problem with yesterday's release that will only affect people using unix and perl 5.6 (or earlier). If you fall into that category, it will be clear because the package should install without a problem, but then Athena and/or Artemis will die without starting and issue an error about not being able to find the "longmess" function. I made a new tar ball and uploaded it to my web site and to SourceForge. There is only one small change in this release compared to the previous one and it will be completely transparent (I think!) for those using perl 5.8. There is *no need* to upgrade your perl installation just to run this release of my software. Of course, if anyone else runs into any problems, let me know. Thanks to Markus Janousch for an excellent bug report and for quickly testing the solution. B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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new release of Athena and Artemis
by Bruce Ravel 09 Mar '04

09 Mar '04

Hi folks, I am announcing the release Athena 0.8.025 and Artemis 0.7.000. You can now run the Windows updater or the horae_update script on your unix machnies to install these new versions. Complete lists of changes can be found in the change logs on my web site. I have increased the minor version number of Artemis because of two significant new features. 1. Atoms is now incorporated into Artemis and there is a simple wrapper around Feff built into Artemis. You no longer need to run Atoms and Feff apart from Artemis. Instead, you now do these chores within Artemis and allow Artemis to organize and manage all of the output files from Feff. By default, Artemis assumes you will be using the version of feff6 that comes with Ifeffit (but that is configurable). 2. Artemis project files are now zip files which contain all data and feff files along with the description of the fitting model. This means that it is easy to share analysis projects with friends and to move analysis projects between computers. The project files are normal zip files that can be examined with PKZip, WinZip, StuffIt, ark, or File Roller. To explain these changes more fully, I have added a chapter to the draft document for Artemis. See chapter 5 in the PDF file at: http://leonardo.phys.washington.edu/~ravel/software/exafs/docs.html Please read this new chapter as it explains the features in full detail. As always, let me know about any bugs, questions, or suggestions. This is a significant new direction for Artemis, so I look forward to hearing about the issues that will, no doubt, come up. You can thank Adam Webb and Paul Fons for all the bugs that *aren't* in Artemis due to their excellent feedback on the new version. B -- ********* PLEASE NOTE MY NEW PHONE, FAX, & ROOM NUMBERS ****************** Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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athena 0.8.026 and artemis 0.7.001
by Bruce Ravel 09 Mar '04

09 Mar '04

Hi folks, New versions of Athena and Artemis are now ready. The windows and unix updater programs will now grab and install these updates. This release addresses many bugs that were found in the previous release. There are also a couple of nice things for the Windows users. I recently upgraded by license for the PerlApp program, which is the program which builds the Windows executables from the perl source code. The new version of PerlApp has the very nice feature of generating *much* smaller executables -- Athena is about 2 megs as compared to about 5 megs from the previous version of PerlApp. There are two big new features in this release. 1. Athena now has an interface for doing linear combination fits of standard XANES spectra to an unknown. Look in the Analysis menu. 2. Both Athena and Artemis have a new mechanism for trapping certain kinds of errors and writing files that can be included in a bug report. If a certain class of problem gets tripped while you are using one of the codes, the program will beep and you will see a message like this in the echo area: Artemis trapped a warning! Message dumped to C:\Program Files\Ifeffit\horae\ARTEMIS.TRAP If you decide to send me a bug report regarding whatever lead to the error, you should include the specified file along with your bug report. The trap file may look cryptic, but it will probably help me a lot in solving the problem. Update and enjoy! B P.S. Big thanks this time for excellent bug reports from Peter Southon, Peter Pfalzer, and valient beta tester Adam Webb. Thanks also to Simon Bare for his help with the linear combination interface. -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Ins:[Ifeffit] Re: problems with the new version-solved
by ALAM Sher 09 Mar '04

09 Mar '04

Hi, Maybe this can be of help.... I had a problem with horae-030, which I solved.... Before when I installed horae-029 there were no problems. Please note that I am using Red Hat Linux The problem was that in directory Ifeffit under horae-030 there are files Group.pm and Path.pm, used respectively by athena and artemis....The version numbers of these did NOT coincide with those in the same files in directory /usr/lib/perl/perl_site/5. /Group.pm etc..... Thus I fixed the numbers in the above files and problem was solved..... Perhaps the problem can be conflicting verion numbers thanks sher > On Friday 05 March 2004 12:14 pm, Giuliana Aquilanti wrote: > > Hi Bruce, > > > > I am trying to get the new versions of Athena and Artemis. > > I cliccked on updater.exe but I continued having > > Athena 0.8.024 and Artemis 0.6.009. > > After I installed from zero ifeffit-1.2.5a.exe and the > > ifeffit_updater-1.1.exe but I have still the old versions. > > ...I don't understand.... > > Hi Giuliana, > > I don't think I understand either. If you have installed > ifeffit-1.2.5a.exe then the next time you run athena or artemis, the > installer should notice that you are not up to date. You certainly > are not -- I released Athena 0.8.025 and Artemis. 0.7.000 after Matt > released ifeffit-1.2.5a.exe. I was counting on the updater to do its > thing. > > However, if you are behind a firewall (which is, as I recall, the case > at ESRF), the firewall may obstruct the updater program. > > I don't know the solution to that problem, but I have taken the > liberty of CCing this to the mailing list. Perhaps someone else will > have some wisdom to share.... > > B > > > -- > Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu > Code 6134, Building 3, Room 405 > Naval Research Laboratory phone: (1) 202 767 2268 > Washington DC 20375, USA fax: (1) 202 767 4642 > > NRL Synchrotron Radiation Consortium (NRL-SRC) > Beamlines X11a, X11b, X23b > National Synchrotron Light Source > Brookhaven National Laboratory, Upton, NY 11973 > > My homepage: http://feff.phys.washington.edu/~ravel > EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/ > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Re: problems with the new version
by Bruce Ravel 05 Mar '04

05 Mar '04

On Friday 05 March 2004 12:14 pm, Giuliana Aquilanti wrote: > Hi Bruce, > > I am trying to get the new versions of Athena and Artemis. > I cliccked on updater.exe but I continued having > Athena 0.8.024 and Artemis 0.6.009. > After I installed from zero ifeffit-1.2.5a.exe and the > ifeffit_updater-1.1.exe but I have still the old versions. > ...I don't understand.... Hi Giuliana, I don't think I understand either. If you have installed ifeffit-1.2.5a.exe then the next time you run athena or artemis, the installer should notice that you are not up to date. You certainly are not -- I released Athena 0.8.025 and Artemis. 0.7.000 after Matt released ifeffit-1.2.5a.exe. I was counting on the updater to do its thing. However, if you are behind a firewall (which is, as I recall, the case at ESRF), the firewall may obstruct the updater program. I don't know the solution to that problem, but I have taken the liberty of CCing this to the mailing list. Perhaps someone else will have some wisdom to share.... B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Chi^2-Map question
by Norbert Weiher 04 Mar '04

04 Mar '04

Dear Friends, maybe some of you remember that I was implementing a chi^2 mapping algorithm using the IFEFFIT library. This is working now, and for the data analysis of the maps I would like to ask your opinion on the following problem: I want to check with chi^2 maps if I can separate 2 shells, e.g. if a peak is comprising two O shells or only one. For this I take the one-shell fit, half the coordination number and then vary the distance of the shells against each other (all other values taking from the best single shell fit). If I find two contributions, I should see 2 mirror-symmetric minima centered at the corresponding DR values, e.g. (0,-0.1) and (-0.1,0) if I work with the same reference. These minima are separated by a saddle point which is more or less pronounced. In the case of some Fe complexes I simulated, it is clearly visible, while for my gold oxides, it is hardly seen but still there. If I take a system where I know there IS only one shell (e.g. Au metal) and do the map, I find no saddle point and correspondingly no 2 minima. Does anyone know a relation between the height of a saddle point and the physical significance of the map? I would be glad to learn more about, but the statistic books I know don't deal with such a problem (and I am chemist and not a mathematician)... If you need an example, I can send you two slides of a recent talk which explain this problem more in detail - just drop me a mail. Cheers, Norbert -- Dr. rer. nat. Norbert Weiher (weiher(a)chem.ethz.ch) Institute for Chemical and Bioengineering - ETH Hönggerberg HCI E 117 - 8093 Zürich - Phone: +41 1 63 3 48 32

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RE: XAFS 12
by Wojciech Gawelda 04 Mar '04

04 Mar '04

Hi Bruce, I wondered about the same thing but it seems like editors of Physica Scripta are very reluctant to say anything. I tried repeatedly to send e-mails to them asking about any approximation when the topical issue on XAFS 12 will come out but I got no response. So it seems like we have to patiently wait and check their web site from time to time. I know it doesn't sound great... Greetings, Wojciech Gawelda ********************************************************************* Wojciech Gawelda Laboratoire de Spectroscopie Ultrarapide (LSU) Institut des Sciences et Ingénierie Chimiques (ISIC), Faculté des Sciences de Base (SB-BSP) Ecole Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne-Dorigny, Switzerland Tel.: +41 (21) 693 0452 Fax.: +41 (21) 693 0422 E-mail: wojciech.gawelda(a)epfl.ch WWW: http://lsu.epfl.ch ********************************************************************* -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: mercredi, 3. mars 2004 19:00 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 13, Issue 3 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. references for fluorescence corrections (Grant Bunker) 2. XAFS12 (Bruce Ravel) 3. Chi^2-Map question (Norbert Weiher) ---------------------------------------------------------------------- Message: 1 Date: Tue, 2 Mar 2004 22:21:17 -0600 (CST) From: Grant Bunker <bunker(a)biocat1.phys.iit.edu> Subject: [Ifeffit] references for fluorescence corrections To: ifeffit(a)millenia.cars.aps.anl.gov Message-ID: <Pine.LNX.4.44.0403022219160.32516-100000(a)biocat1.phys.iit.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII Greetings, All - I'll make another effort to get this by the ANL Spam filters. A references for fluorescence corrections can be found in Booth and Bridge's paper http://xxx.lanl.gov/abs/cond-mat/0306252 they have refs to earlier work also. thanks - grant On Tue, 2 Mar 2004 ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: question about S02 (passive electron reduction factor) > (Matt Newville) > 2. *****SPAM***** references for self-absorption correction > (Grant Bunker) > 3. Correlations (Scott Calvin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 1 Mar 2004 12:16:38 -0600 (CST) > From: Matt Newville <newville(a)cars.uchicago.edu> > Subject: Re: [Ifeffit] question about S02 (passive electron reduction > factor) > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <Pine.LNX.4.44.0403011211200.10753-100000(a)millenia.cars.aps.anl.gov> > Content-Type: TEXT/PLAIN; charset=US-ASCII > > Hi Scott, > > First, I'm not sure how your message got tagged as Spam by Argonne's > SpamAssassin (words or phrases selling drugs??? huh???), but that > happens well before I can do anything about it. I've forwarded this > message on as a false positive for spam. For better archiving, I > also included the full message you sent below. > > > Good point. It is much more straightforward to check the uncertainty than > > the correlation to determine if that could be responsible for the > > anomalous S02...so I should have said that Yu-Chuan should check the > > uncertainty of the S02 parameter. If it is very large (say 0.8), then > > Ifeffit is in effect reporting that it cannot determine S02 well for some > > reason. At that point, I think it is helpful to see if there is a high > > correlation, since that may give a clue as to the reason for the large > > uncertainty. > > Knowing the correlations always helps. And stating a best-fit value > without an uncertainty is dangerous (one might take an implicit > uncertainty, which may not be what you mean). > > This is probably a bit off-topic from the original question (where > I'd guess self-absorption to be the main issue,....), but let's > consider typical fit results: S02= 0.9 +/- 0.1, sigma2= 0.015 +/- > 0.005, and a correlation between S02 and sigma2 C_S02_sigma2= +0.90. > One could conclude from these that a true value of S02= 1.0 was > reasonable. But in order to get to S02= 1.0, sigma2 has to go up to > ~= 0.019 (~= sigma2_best + C_S02_sigma2 * delta_sigma2). S02= 0.80 > is also reasonable, but this implies sigma2 would drop to around > 0.011. The correlation means that, although having either S02= 0.80 > OR sigma2= 0.020 would be reasonable,t having both S02= 0.80 AND > sigma2= 0.020 is much less likely. > > The correlation by itself says nothing about the likelihood of > having a true value for S02 of, say, 0.5. There is a chance this > can happen, but it's small because the uncertainty in S02 is 0.1. > The correlation simply tells you how sigma2 would respond if S02 > were 0.5, but nothing more. > > > So this brings up a (possibly contentious) point. In their reporting > > recommendations, the IXS suggests reporting high correlations, > > particularly when they are between parameters that do not routinely show > > high correlations. What is the reason for this suggestion? I'm not > > criticizing it...just looking for the rationale. > > It's hard to speak for the IXS, but I'd say that correlations are > recommended to be reported because they're important statistics. The > correlations, along with the best-fit values and uncertainties, help > more fully describe the range of plausible results. > > It's generally well-known that the parameters (S02,sigma2) and > (E0,R) are highly correlated for a single shell of a single data > set, and the implications of these are generally understood, I > think. Sometimes other variables are correlated, and some people > even do complex fits with multiple data sets or generalized > variables that are not the simple XAFS parameters ;). In these > cases, it may not be obvious how the variables are correlated. I > think the IXS committee was concerned about this, and so recommended > reporting correlations in such cases. That seems sensible to me. > > --Matt > > > > On Sat, 28 Feb 2004, Scott Calvin wrote: > > > > Matt, > > > > Good point. It is much more straightforward to check the uncertainty than > > the correlation to determine if that could be responsible for the anomalous > > S02...so I should have said that Yu-Chuan should check the uncertainty of > > the S02 parameter. If it is very large (say 0.8), then Ifeffit is in effect > > reporting that it cannot determine S02 well for some reason. At that point, > > I think it is helpful to see if there is a high correlation, since that may > > give a clue as to the reason for the large uncertainty. > > > > So this brings up a (possibly contentious) point. In their reporting > > recommendations, the IXS suggests reporting high correlations, particularly > > when they are between parameters that do not routinely show high > > correlations. What is the reason for this suggestion? I'm not criticizing > > it...just looking for th erationale. > > > > --Scott Calvin > > Sarah Lawrence College > > > > > ------------------------------ > > Message: 2 > Date: Mon, 1 Mar 2004 13:53:53 -0600 (CST) > From: Grant Bunker <bunker(a)biocat1.phys.iit.edu> > Subject: [Ifeffit] *****SPAM***** references for self-absorption > correction > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: > <Pine.LNX.4.44.0403011343220.6220-100000(a)biocat1.phys.iit.edu> > Content-Type: text/plain; charset="us-ascii" > > -------------------- Start SpamAssassin results ---------------------- > Content analysis details: (7.1 hits, 5.6 required) > -4.9 BAYES_00 BODY: Bayesian spam probability is 0 to 1% > [score: 0.0000] > 6.0 PORN_4 URI: URL uses words/phrases which indicate porn > 6.0 DRUGS_APS BODY: Words and phrases selling drugs > > -------------------- End of SpamAssassin results --------------------- > > >

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XAFS12
by Bruce Ravel 03 Mar '04

03 Mar '04

Hi folks! Does anyone have any information on when the volume of Physica Scripta containing the proceedings of the last XAFS conference will be published? Is there at least a volume number yet? Thanks, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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references for fluorescence corrections
by Grant Bunker 03 Mar '04

03 Mar '04

Greetings, All - I'll make another effort to get this by the ANL Spam filters. A references for fluorescence corrections can be found in Booth and Bridge's paper http://xxx.lanl.gov/abs/cond-mat/0306252 they have refs to earlier work also. thanks - grant On Tue, 2 Mar 2004 ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: question about S02 (passive electron reduction factor) > (Matt Newville) > 2. *****SPAM***** references for self-absorption correction > (Grant Bunker) > 3. Correlations (Scott Calvin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 1 Mar 2004 12:16:38 -0600 (CST) > From: Matt Newville <newville(a)cars.uchicago.edu> > Subject: Re: [Ifeffit] question about S02 (passive electron reduction > factor) > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <Pine.LNX.4.44.0403011211200.10753-100000(a)millenia.cars.aps.anl.gov> > Content-Type: TEXT/PLAIN; charset=US-ASCII > > Hi Scott, > > First, I'm not sure how your message got tagged as Spam by Argonne's > SpamAssassin (words or phrases selling drugs??? huh???), but that > happens well before I can do anything about it. I've forwarded this > message on as a false positive for spam. For better archiving, I > also included the full message you sent below. > > > Good point. It is much more straightforward to check the uncertainty than > > the correlation to determine if that could be responsible for the > > anomalous S02...so I should have said that Yu-Chuan should check the > > uncertainty of the S02 parameter. If it is very large (say 0.8), then > > Ifeffit is in effect reporting that it cannot determine S02 well for some > > reason. At that point, I think it is helpful to see if there is a high > > correlation, since that may give a clue as to the reason for the large > > uncertainty. > > Knowing the correlations always helps. And stating a best-fit value > without an uncertainty is dangerous (one might take an implicit > uncertainty, which may not be what you mean). > > This is probably a bit off-topic from the original question (where > I'd guess self-absorption to be the main issue,....), but let's > consider typical fit results: S02= 0.9 +/- 0.1, sigma2= 0.015 +/- > 0.005, and a correlation between S02 and sigma2 C_S02_sigma2= +0.90. > One could conclude from these that a true value of S02= 1.0 was > reasonable. But in order to get to S02= 1.0, sigma2 has to go up to > ~= 0.019 (~= sigma2_best + C_S02_sigma2 * delta_sigma2). S02= 0.80 > is also reasonable, but this implies sigma2 would drop to around > 0.011. The correlation means that, although having either S02= 0.80 > OR sigma2= 0.020 would be reasonable,t having both S02= 0.80 AND > sigma2= 0.020 is much less likely. > > The correlation by itself says nothing about the likelihood of > having a true value for S02 of, say, 0.5. There is a chance this > can happen, but it's small because the uncertainty in S02 is 0.1. > The correlation simply tells you how sigma2 would respond if S02 > were 0.5, but nothing more. > > > So this brings up a (possibly contentious) point. In their reporting > > recommendations, the IXS suggests reporting high correlations, > > particularly when they are between parameters that do not routinely show > > high correlations. What is the reason for this suggestion? I'm not > > criticizing it...just looking for the rationale. > > It's hard to speak for the IXS, but I'd say that correlations are > recommended to be reported because they're important statistics. The > correlations, along with the best-fit values and uncertainties, help > more fully describe the range of plausible results. > > It's generally well-known that the parameters (S02,sigma2) and > (E0,R) are highly correlated for a single shell of a single data > set, and the implications of these are generally understood, I > think. Sometimes other variables are correlated, and some people > even do complex fits with multiple data sets or generalized > variables that are not the simple XAFS parameters ;). In these > cases, it may not be obvious how the variables are correlated. I > think the IXS committee was concerned about this, and so recommended > reporting correlations in such cases. That seems sensible to me. > > --Matt > > > > On Sat, 28 Feb 2004, Scott Calvin wrote: > > > > Matt, > > > > Good point. It is much more straightforward to check the uncertainty than > > the correlation to determine if that could be responsible for the anomalous > > S02...so I should have said that Yu-Chuan should check the uncertainty of > > the S02 parameter. If it is very large (say 0.8), then Ifeffit is in effect > > reporting that it cannot determine S02 well for some reason. At that point, > > I think it is helpful to see if there is a high correlation, since that may > > give a clue as to the reason for the large uncertainty. > > > > So this brings up a (possibly contentious) point. In their reporting > > recommendations, the IXS suggests reporting high correlations, particularly > > when they are between parameters that do not routinely show high > > correlations. What is the reason for this suggestion? I'm not criticizing > > it...just looking for th erationale. > > > > --Scott Calvin > > Sarah Lawrence College > > > > > ------------------------------ > > Message: 2 > Date: Mon, 1 Mar 2004 13:53:53 -0600 (CST) > From: Grant Bunker <bunker(a)biocat1.phys.iit.edu> > Subject: [Ifeffit] *****SPAM***** references for self-absorption > correction > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: > <Pine.LNX.4.44.0403011343220.6220-100000(a)biocat1.phys.iit.edu> > Content-Type: text/plain; charset="us-ascii" > > -------------------- Start SpamAssassin results ---------------------- > Content analysis details: (7.1 hits, 5.6 required) > -4.9 BAYES_00 BODY: Bayesian spam probability is 0 to 1% > [score: 0.0000] > 6.0 PORN_4 URI: URL uses words/phrases which indicate porn > 6.0 DRUGS_APS BODY: Words and phrases selling drugs > > -------------------- End of SpamAssassin results --------------------- > > >

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Correlations
by Scott Calvin 01 Mar '04

01 Mar '04

Thanks, Matt. That clarifies a few things...in particular, I found the example you gave (quoted below) to be quite helpful. --Scott Calvin Sarah Lawrence College At 12:16 PM 3/1/2004 -0600, you wrote: >This is probably a bit off-topic from the original question (where >I'd guess self-absorption to be the main issue,....), but let's >consider typical fit results: S02= 0.9 +/- 0.1, sigma2= 0.015 +/- >0.005, and a correlation between S02 and sigma2 C_S02_sigma2= +0.90. >One could conclude from these that a true value of S02= 1.0 was >reasonable. But in order to get to S02= 1.0, sigma2 has to go up to >~= 0.019 (~= sigma2_best + C_S02_sigma2 * delta_sigma2). S02= 0.80 >is also reasonable, but this implies sigma2 would drop to around >0.011. The correlation means that, although having either S02= 0.80 >OR sigma2= 0.020 would be reasonable,t having both S02= 0.80 AND >sigma2= 0.020 is much less likely. >> >--Matt > >

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