Dan Carter wrote:
Thats great about the R-factor, I was very impressed to see it so low. Reduced Chi-square = 382.556284248 R-factor = 0.015036203 (fit I started with--two e0's: one for 1st path/1 for others)
I'm wasn't positive about how to use the third cumulant. So, I made a variable third to guess in that position for the first path (the nearest neighbor, right). Here are the results: Reduced Chi-square = 415.039996182 R-factor = 0.014768538 third = 0.000045 (Can you tell if this is a better fit from the Reduced
Chi-square)
If I separate ss's for the first path and the others (leaving the
third
parameter) I get this: Reduced Chi-square = 462.878645915 R-factor = 0.014748364 (not much improvement)
One more thing, for the mailing list: How can I find out if it is ok to separate the e0's of the nearest neighbor from the others?
Thanks, Dan
IFeffit list: OK...you're all caught up on this conversation! Hi Dan, You're approaching this the right way, in general. The answer to how you know whether some change in constraints is worth-while involves the following issues: --Does it make the fit better statistically? One way to do this is see if it decreases the reduced chi-square noticeably. --Is there a justification for the constraints you have chosen? Haphazardly changing the way you constrain parameters may occasionally result in a statistical improvement <italic>by chance</italic>. There are, after all, lots of ways you can imagine splitting up parameters. You had better have some logic behind why the parameters <italic>might</italic> split up the way that you are trying. --Are the fitted parameters physically reasonable? It is possible to give Ifeffit enough rope to hang itself, so to speak. By introducing additional guessed parameters, Ifeffit might be able to find a statistically reasonable but completely unphysical solution (a "false minimum"). Remember, Ifeffit's job is not to find the <italic>correct</italic> structure, it is to find the structure that gives the closest match between fit and data. It's <italic>your</italic> job to evaluate whether the resulting structure is physically reasonable or not. Examples of unreasonableness are things like bonds shorter than any known bond, etc.. In some cases Artemis will flag you on this kind of thing, but it really does (and should) remain the fitter's responsibility. Another comment--provide uncertainties on your numbers! I have no idea if the third cumulant the fit found is significantly different from zero. My impression from the reduced chi-squares, though, is that the third cumulant is not helping you, and can probably be safely set back to zero. So at this point I'd say you have pretty good evidence you have the hexagonal phase as opposed to the trigonal phase. In fact, do you still need the two separate E0's in this phase, or was that just because the fit was having trouble with the trigonal model? --Scott Calvin Sarah Lawrence College At 01:19 PM 8/17/2004 -0400, you wrote:
Dan Carter wrote:
Thats great about the R-factor, I was very impressed to see it so
low.
Reduced Chi-square = 382.556284248
R-factor = 0.015036203
(fit I started with--two e0's: one for 1st path/1 for
others)
I'm wasn't positive about how to use the third cumulant. So, I
made a
variable third to guess in that position for the first path (the nearest
neighbor, right). Here are the results:
Reduced Chi-square = 415.039996182
R-factor = 0.014768538
third = 0.000045
(Can you tell if this is a better fit from the Reduced
Chi-square)
If I separate ss's for the first path and the others (leaving
the
third
parameter) I get this:
Reduced Chi-square = 462.878645915
R-factor = 0.014748364
(not much improvement)
One more thing, for the mailing list: How can I find out if it
is
ok to
separate the e0's of the nearest neighbor from the others?
Hi Mailing list, Well, the chief concern I have with my fit now is that I have some negative parameters (delr and e0_1): Guess parameters +/- uncertainties (initial guess): amp = 0.7709790 +/- 0.0631820 e0 = 1.1165150 +/- 1.0100360 delr = -0.0106440 +/- 0.0077110 ss = 0.0032510 +/- 0.0005200 e0_1 = -4.6848070 +/- 1.7781210 third = 0.0000370 +/- 0.0001070 So, I guess I can drop the third cumulant. This is a fit using 6 paths (1,2,3,6 are single scatterers) These are the results this time around: Reduced Chi-square = 410.285252396 R-factor = 0.014599348 As you can see I am still using two e0's, it is still dramatically improving the fit. Without: Reduced Chi-square = 1133.485950636 R-factor = 0.044551155 any advice welcomed, Dan
Hello folks, just to report on something strange consistently happening to me using Artemis 0.7.008. Ifeffit 1.2.5 (horae 38). Let's say that I want to have a look at the statistics from three fits and compare them using the saved log files. I then click on the Edit->View log files and click on New List. I then get a dialogue window that I can navigate a select the first log file I want to insert in the list using the accept button Then, let's say that the second log file is in another directory: I click on Add logfiles to list and get again the navigation window where I select another log file in another directory. When I then click on accept, I receive a burp from Artemis and the following message: Tk::Error: element "top" already exists at /Library/Perl/5.8.1/darwin-thread-m ti-2level/Tk.pm line 247. Tk callback for .frame3.canvas5.labframe.border.frame1.frame.hlist Tk::__ANON__ at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk.pm line 247 Tk::Derived::Delegate at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk/De ved.pm line 469 Tk::Widget::__ANON__ at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk/Wid t.pm line 322 main::logview_fill_listbox at /Applications/Ifeffit/bin/artemis line 12514 Tk callback for .frame3.canvas5.labframe.border.frame1.button Tk::__ANON__ at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk.pm line 247 Tk::Button::butUp at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk/Button m line 111 <ButtonRelease-1> (command bound to event) main::__ANON__('Tk::Error: element "top" already exists at /Library/Pe /5.8....') called at blib/lib/Tk.pm (autosplit into blib/lib/auto/Tk/Error.al) ine 488 Tk::Error('MainWindow=HASH(0x8f734)','element "top" already exists at ibrary/Perl/5.8.1/darwin-th...','Tk callback for .frame3.canvas5.labframe.bord ..frame1.frame....','Tk::__ANON__ at /Library/Perl/5.8.1/darwin-thread-multi-2l e...','Tk::Derived::Delegate at /Library/Perl/5.8.1/darwin-thread-mu...','Tk:: dget::__ANON__ at /Library/Perl/5.8.1/darwin-thread-mul...','main::logview_fil listbox at /Applications/Ifeffit/bin/artem...','Tk callback for .frame3.canvas labframe.border.frame1.button','Tk::__ANON__ at /Library/Perl/5.8.1/darwin-thr d-multi-2leve...',...) called at /Library/Perl/5.8.1/darwin-thread-multi-2leve Tk/Widget.pm line 932 eval {...} called at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk idget.pm line 932 Tk::Widget::waitVariable('Tk::FileSelect=HASH(0x1336d064)','SCALAR(0x1 c1604)') called at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk/FileSelec pm line 550 Tk::FileSelect::Show('Tk::FileSelect=HASH(0x1336d064)') called at /App cations/Ifeffit/bin/artemis line 12502 main::logview_fill_listbox('Tk::Frame=HASH(0x132ca90c)','add') called /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk.pm line 247 eval {...} called at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk m line 247 Tk::__ANON__('Tk::Button=HASH(0x1399f494)') called at /Library/Perl/5. 1/darwin-thread-multi-2level/Tk/Button.pm line 111 Tk::Button::butUp('Tk::Button=HASH(0x1399f494)') called at /Library/Pe /5.8.1/darwin-thread-multi-2level/Tk.pm line 406 eval {...} called at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk m line 406 Tk::MainLoop() called at /Applications/Ifeffit/bin/artemis line 1792 This is not a major problem, because if I put the log files I wish to compare in the same directory the accept button runs smootly when I select multiple files, but it would be convenient to select also files residing in different directories. Hola, Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI "Ihr seid bestimmt, nicht Tieren gleich zu leben, Nein, Tugend zu erringen und Erkenntnis" "Ye were not form'd to live the life of brutes, But virtue to pursue and knowledge high"
On Monday 23 August 2004 10:41 am, Stefano Ciurli wrote:
Let's say that I want to have a look at the statistics from three fits and compare them using the saved log files. I then click on the Edit->View log files and click on New List. I then get a dialogue window that I can navigate a select the first log file I want to insert in the list using the accept button Then, let's say that the second log file is in another directory: I click on Add logfiles to list and get again the navigation window where I select another log file in another directory. When I then click on accept, I receive a burp from Artemis and the following message:
The log viewer in the current Artemis is a very crude hack. If you find that it works -- great! If not -- sorry! As a workaround to this problem, I'd recommend putting (or symlinking) all your log files into a single directory. You might consider the location which is the default when you save a log file, which is in the project work space. As I mentioned a while back, I have split Artemis into stable and development branches. The log viewer is currently being rewritten and will take on a very central role in the future in Artemis. Since this feature is changing so dramatically, I am disinclined to work too hard on the log viewer in the stable branch -- particularly if a simple enough work-around exists. B -- Bruce Ravel ----------------------------------- ravel@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/
Hello Bruce, yes, fortunately there is a way around, but just in case this bug was not seen before, I thought of reporting it. Thank you! Ciao! STefano
The log viewer in the current Artemis is a very crude hack. If you find that it works -- great! If not -- sorry!
As a workaround to this problem, I'd recommend putting (or symlinking) all your log files into a single directory. You might consider the location which is the default when you save a log file, which is in the project work space.
As I mentioned a while back, I have split Artemis into stable and development branches. The log viewer is currently being rewritten and will take on a very central role in the future in Artemis. Since this feature is changing so dramatically, I am disinclined to work too hard on the log viewer in the stable branch -- particularly if a simple enough work-around exists.
B
-- Bruce Ravel ----------------------------------- ravel@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@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
-- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI "Ihr seid bestimmt, nicht Tieren gleich zu leben, Nein, Tugend zu erringen und Erkenntnis" "Ye were not form'd to live the life of brutes, But virtue to pursue and knowledge high"
Bruce, another little problem with the log viewer is the fact that not always (random, I have seen it only a couple of times) I can see the option of writing and plotting amp, e0, delr and ss, while all the times the chiquare, reduced chi square and R-factor is visible as option. CIao, Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI "Ihr seid bestimmt, nicht Tieren gleich zu leben, Nein, Tugend zu erringen und Erkenntnis" "Ye were not form'd to live the life of brutes, But virtue to pursue and knowledge high"
On Tuesday 24 August 2004 06:11 am, Stefano Ciurli wrote:
another little problem with the log viewer is the fact that not always (random, I have seen it only a couple of times) I can see the option of writing and plotting amp, e0, delr and ss, while all the times the chiquare, reduced chi square and R-factor is visible as option.
Thanks, Stefano, but same answer as yesterday. ;-) B -- Bruce Ravel ----------------------------------- ravel@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/
participants (4)
-
Bruce Ravel -
dmc＠pdx.edu -
Scott Calvin -
Stefano Ciurli