It would be the best to store results of each iterations in convergence(). I already had a couple of cases / models that never converged. Predominately, these were molecules with a high degree o motion. For example there was a peptide (40 residues), where none of the models converged after 20 iterations, so I aborted them. The diffusion tensor fits well so I thought that's alright. I heard from other people that they also stop their calculation after 20 iterations. Nevertheless and surprisingly, the model wich was selected for S2 (And the rest) was local tm - possible?
But in general I like the idea to compare the minimization of all the iterations, as you suggested. I still would set a maximum of 20 (or 30) iterations to avoid calculations over several days. Another benefit is that we are able to update the progress bar. Edward d'Auvergne wrote: > Hi Michael, > > We could add an arg to limit the number of iterations, but I think > there is a much better way. The problem of iterating forever is > because of circling around the minimum (not the optimisation minimum > but Occam's razor, as described in equation (14) of my 2007 paper > http://www.nmr-relax.com/refs.html). Currently only the current to > previous iterations are compared, but some people have encountered a 3 > iteration cycle. Even larger looping might occur. Note that the > repeated position in this cycle is identical to one of the previous. > So we should really store all of the required info in the > convergence() method of auto_analyses/dauvergne_protocol.py and check > the current against all iterations. > > If one of these converged loops has not been reached after 20 > iterations, then either the system is complex but will still soon > converge, or something is seriously, very seriously wrong. The model > should be deselected and the user told of its total failure. My > experience is that after 20, convergence has been reached. But I > think we should allow more before termination, as the termination is a > sign that something is sick. > > If we catch the large iteration circling about Occam's razor and > terminate, do you think we would need a maximum iteration termination > point and subsequent global model elimination? Have you encountered > such a non-cycling, infinite looping? > > Regards, > > Edward > > > > > On 12 April 2010 03:02, <[email protected]> wrote: > >> Author: michaelbieri >> Date: Mon Apr 12 03:02:19 2010 >> New Revision: 11061 >> >> URL: http://svn.gna.org/viewcvs/relax?rev=11061&view=rev >> Log: >> The relaxGUI controller updates its progress bar using informations from the >> status singleton during model-free analysis. >> >> Currently, there is a maximum of iterations set for models 1 - 5. This also >> has to be set in the dauvergne_protocol.py script. Edward, what do you think >> about limiting to 20 iterations? >> >> Modified: >> branches/bieri_gui/gui_bieri/controller.py >> >> Modified: branches/bieri_gui/gui_bieri/controller.py >> URL: >> http://svn.gna.org/viewcvs/relax/branches/bieri_gui/gui_bieri/controller.py?rev=11061&r1=11060&r2=11061&view=diff >> ============================================================================== >> --- branches/bieri_gui/gui_bieri/controller.py (original) >> +++ branches/bieri_gui/gui_bieri/controller.py Mon Apr 12 03:02:19 2010 >> @@ -142,13 +142,50 @@ >> >> def __init__(self,aWxTextCtrl): >> self.out=aWxTextCtrl >> + self.status = Status() >> >> + def limit_entries(self): >> + """ Function to overcome feedback problem of wx.CallAfter() >> command""" >> + >> + # Maximum allowed number of lines in log window. >> + max_entries = 10000 >> + >> + # read number of lines in log window. >> + total_entries = self.out.log_panel.GetNumberOfLines() >> + >> + # Shift entries backwards if maximum of line exeeded. >> + if total_entries > max_entries: >> + # Reset log window entries >> + new_entries = 'Refreshing log window...\n\n' >> + self.out.log_panel.SetValue(new_entries) >> >> def write(self,string): >> - global progress >> >> # Limit panle entries to max_entries Lines. >> wx.CallAfter(self.limit_entries) >> + >> + # Update Gauge (Progress bar). >> + # Local tm model: >> + if self.status.dAuvergne_protocol.diff_model == 'local_tm': >> + # Current model. >> + no = self.status.dAuvergne_protocol.current_model[2:] >> + no = int(no) >> + >> + # Total selected models. >> + total_models = >> len(self.status.dAuvergne_protocol.local_mf_models) >> + >> + # update Progress bar. >> + wx.CallAfter(self.out.progress_bar.SetValue, >> (100*no/total_models)) >> + >> + # Sphere to Ellipsoid Models. >> + if self.status.dAuvergne_protocol.diff_model in ['sphere', >> 'prolate', 'oblate', 'ellipsoid']: >> + # Determine actual round (maximum is 20). >> + wx.CallAfter(self.out.progress_bar.SetValue, >> (100*(self.status.dAuvergne_protocol.round-1)/20)) >> + >> + # Final analysis. >> + if self.status.dAuvergne_protocol.diff_model == 'final': >> + mc_simulation = self.status.mc_number >> + >> >> # Add new output. >> wx.CallAfter(self.out.log_panel.AppendText, string) >> >> >> _______________________________________________ >> relax (http://nmr-relax.com) >> >> This is the relax-commits mailing list >> [email protected] >> >> To unsubscribe from this list, get a password >> reminder, or change your subscription options, >> visit the list information page at >> https://mail.gna.org/listinfo/relax-commits >> >> > > _______________________________________________ > relax (http://nmr-relax.com) > > This is the relax-devel mailing list > [email protected] > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-devel > > > _______________________________________________ relax (http://nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
