That's probably the correct solution. And then pC would be zero by default.
Regards, Edward On 19 August 2014 18:44, Troels Emtekær Linnet <tlin...@nmr-relax.com> wrote: > I can set it 1 - pA? > > Best > Troels > > 2014-08-19 18:13 GMT+02:00 Edward d'Auvergne <edw...@nmr-relax.com>: >> That would be the correct behaviour without optimisation. Hmmm, what >> was pB set to in this case originally? Maybe we need to set pB to 0 >> to start with, and then let it optimise away from this. What do you >> think? >> >> Regards, >> >> Edward >> >> >> >> On 19 August 2014 18:06, Troels Emtekær Linnet <tlin...@nmr-relax.com> wrote: >>> Hi Edward. >>> >>> 'r2', 'pA', 'dw', 'kex' >>> >>> I then read this as: >>> >>> self.assertEqual(par_dic['r2'], 'r2') >>> self.assertEqual(par_dic['pA'], 'pA') >>> self.assertEqual(par_dic['dw_AB'], 'dw') >>> self.assertEqual(par_dic['kex_AB'], 'kex') >>> self.assertEqual(par_dic['pB'], None) >>> self.assertEqual(par_dic['dw_BC'], 'dw') >>> self.assertEqual(par_dic['kex_BC'], 'kex') >>> self.assertEqual(par_dic['kex_AC'], 'kex') >>> >>> Best >>> Troels >>> >>> 2014-08-19 17:42 GMT+02:00 Edward d'Auvergne <edw...@nmr-relax.com>: >>>> Hi, >>>> >>>> I saw that the code has evolved to do this. The original idea and >>>> implementation was to set states B and C to the same values of the >>>> 2-state model parameters and then let them drift apart. This was >>>> mentioned in the manual. This is not great, but the alternative of >>>> performing a grid search on 'dw_AB', 'kex_AB', 'pB', 'dw_BC', >>>> 'kex_BC', 'kex_AC' is worse - this grid search is just impossibly long >>>> if you choose a reasonable number of grid increments. Being a >>>> multi-minima problem also invalidates this. The grid search and local >>>> optimisation is only for single minimum problems. When multiple >>>> minima are present, then global algorithms are required (the main ones >>>> are simulated annealing and genetic algorithms, neither of which are >>>> present in minfx yet and hence relax). Therefore setting B and C to >>>> the same thing is not too unreasonable considering the alternative >>>> issues. >>>> >>>> The same thing was done for the '* full' models. The value of R20 was >>>> copied to R20A and R20B and then the two allowed to drift apart. This >>>> is also an incredibly difficult optimisation problem with possible >>>> multiple minima. >>>> >>>> There is no perfect solution for the R20A != R20B or 3-site models yet. >>>> >>>> Regards, >>>> >>>> Edward >>>> >>>> >>>> >>>> On 19 August 2014 17:21, Troels Emtekær Linnet <tlin...@nmr-relax.com> >>>> wrote: >>>>> Hi Edward. >>>>> >>>>> >>>>> Just to confirm. >>>>> >>>>> If the model is: MODEL_PARAMS_NS_R1RHO_3SITE >>>>> And the nested model is: MODEL_PARAMS_NS_R1RHO_2SITE >>>>> >>>>> The possible parameters for conversion are: >>>>> self.assertEqual(par_dic['r2'], 'r2') >>>>> self.assertEqual(par_dic['pA'], 'pA') >>>>> self.assertEqual(par_dic['dw_AB'], None) >>>>> self.assertEqual(par_dic['kex_AB'], None) >>>>> self.assertEqual(par_dic['pB'], None) >>>>> self.assertEqual(par_dic['dw_BC'], None) >>>>> self.assertEqual(par_dic['kex_BC'], None) >>>>> self.assertEqual(par_dic['kex_AC'], None) >>>>> >>>>> This means, that MODEL_PARAMS_NS_R1RHO_3SITE would start to Grid Search: >>>>> 'dw_AB', 'kex_AB', 'pB', 'dw_BC', 'kex_BC', 'kex_AC' >>>>> >>>>> Do we agree on this? >>>>> >>>>> Best >>>>> Troels >>>>> >>>>> >>>>> ---------- Forwarded message ---------- >>>>> From: <edw...@nmr-relax.com> >>>>> Date: 2014-08-19 16:07 GMT+02:00 >>>>> Subject: r25077 - /trunk/docs/latex/dispersion.tex >>>>> To: relax-comm...@gna.org >>>>> >>>>> >>>>> Author: bugman >>>>> Date: Tue Aug 19 16:07:37 2014 >>>>> New Revision: 25077 >>>>> >>>>> URL: http://svn.gna.org/viewcvs/relax?rev=25077&view=rev >>>>> Log: >>>>> Added a table for dispersion model nesting in the auto-analysis to the >>>>> manual. >>>>> >>>>> This adds the ideas discussed in the thread >>>>> http://thread.gmane.org/gmane.science.nmr.relax.devel/6684. >>>>> >>>>> >>>>> Modified: >>>>> trunk/docs/latex/dispersion.tex >>>>> >>>>> Modified: trunk/docs/latex/dispersion.tex >>>>> URL: >>>>> http://svn.gna.org/viewcvs/relax/trunk/docs/latex/dispersion.tex?rev=25077&r1=25076&r2=25077&view=diff >>>>> ============================================================================== >>>>> --- trunk/docs/latex/dispersion.tex (original) >>>>> +++ trunk/docs/latex/dispersion.tex Tue Aug 19 16:07:37 2014 >>>>> @@ -1689,8 +1689,9 @@ >>>>> For the cluster specific parameters, i.e.\ the populations of >>>>> the states and the exchange parameters, an average value will be used >>>>> as the starting point. >>>>> For all other parameters, the $\Rtwozero$ values for each spin >>>>> and magnetic field, as well as the parameters related to the chemical >>>>> shift difference $\dw$, the optimised values of the previous run will >>>>> be directly copied. >>>>> \item[Model nesting:] If two models are nested, then the >>>>> parameters of the simpler will be used as the starting point for >>>>> optimisation of the more complex. >>>>> - The currently supported nested model pairs are `LM63' and `LM63 >>>>> 3-site', `CR72' and `CR72 full', `CR72' and `MMQ CR72', `NS CPMG >>>>> 2-site 3D' and `NS CPMG 2-site 3D full', and `NS CPMG 2-site star' and >>>>> `NS CPMG 2-site star full'. >>>>> - In these cases, the $\RtwozeroA$ and $\RtwozeroB$ parameter >>>>> values are set to the simpler model $\Rtwozero$ value and the grid >>>>> search is bypassed. >>>>> + The currently supported nested model sets are presented in >>>>> Table~\ref{table: dispersion model nesting} on page~\pageref{table: >>>>> dispersion model nesting}. >>>>> + The models are optimised in the order presented in that table. >>>>> + In some cases, the $\RtwozeroA$ and $\RtwozeroB$ parameter >>>>> values are set to the simpler model $\Rtwozero$ value and the grid >>>>> search is bypassed. >>>>> \item[Model equivalence:] When two models are equivalent, the >>>>> optimised parameters of one model can be used as the starting point of >>>>> the other rather than performing a grid search. >>>>> This is used in the auto-analysis for avoiding the grid search >>>>> in the numeric models. >>>>> The optimised `CR72' model is used for the `NS CPMG 2-site >>>>> expanded', `NS CPMG 2-site 3D', and `NS CPMG 2-site star' models. >>>>> @@ -1722,6 +1723,103 @@ >>>>> If you are a power user, you are free to use all of the relax user >>>>> functions, the relax library, and the relax data store to implement >>>>> your own protocol. >>>>> If you wish, the protocol can be converted into a new auto-analysis >>>>> and distributed as part of relax. >>>>> The relax test suite will ensure the protocol remains functional for >>>>> the lifetime of relax. >>>>> + >>>>> +\begin{landscape} >>>>> +\begin{center} >>>>> +\begin{small} >>>>> + >>>>> +% The longtable environment. >>>>> +\begin{longtable}{ll} >>>>> + >>>>> +% Caption. >>>>> +\caption{Model nesting for the relaxation dispersion auto-analysis.} >>>>> + >>>>> +% Header. >>>>> +\\ >>>>> +\toprule >>>>> +Model & Nested models\footnotemark[1] \\ >>>>> +\midrule >>>>> +\endhead >>>>> + >>>>> +% Footer. >>>>> +\bottomrule >>>>> +\endfoot >>>>> + >>>>> +% Label. >>>>> +\label{table: dispersion model nesting} >>>>> + >>>>> + >>>>> +% Experiment independent models. >>>>> +\\[-5pt] >>>>> +Base models \\ >>>>> +\cline{1-1} >>>>> +$\Rtwoeff/\Ronerhoprime$ & - \\ >>>>> +No Rex & - \\ >>>>> + >>>>> +% CPMG-type models. >>>>> +\\[-5pt] >>>>> +Single quantum (SQ) CPMG-type \\ >>>>> +\cline{1-1} >>>>> +LM63 & - \\ >>>>> +LM63 3-site & LM63 \\ >>>>> +CR72 & NS CPMG 2-site 3D, NS CPMG 2-site >>>>> star, NS CPMG 2-site expanded, B14 \\ >>>>> +CR72 full & NS CPMG 2-site 3D full, NS CPMG >>>>> 2-site star full, B14 full, NS CPMG 2-site 3D, \\ >>>>> + & NS CPMG 2-site star, NS CPMG >>>>> 2-site expanded, B14, CR72 \\ >>>>> +IT99 & - \\ >>>>> +TSMFK01 & - \\ >>>>> +B14 & NS CPMG 2-site 3D, NS CPMG 2-site >>>>> star, NS CPMG 2-site expanded, CR72 \\ >>>>> +B14 full & NS CPMG 2-site 3D full, NS CPMG >>>>> 2-site star full, CR72 full, NS CPMG 2-site 3D, \\ >>>>> + & NS CPMG 2-site star, NS CPMG >>>>> 2-site expanded, B14, CR72 \\ >>>>> +NS CPMG 2-site expanded & NS CPMG 2-site 3D, NS CPMG 2-site >>>>> star, B14, CR72 \\ >>>>> +NS CPMG 2-site 3D & NS CPMG 2-site star, NS CPMG >>>>> 2-site expanded, B14, CR72 \\ >>>>> +NS CPMG 2-site 3D full & NS CPMG 2-site star full, B14 >>>>> full, CR72 full, NS CPMG 2-site 3D, NS CPMG 2-site star, \\ >>>>> + & NS CPMG 2-site expanded, B14, CR72 \\ >>>>> +NS CPMG 2-site star & NS CPMG 2-site 3D, NS CPMG 2-site >>>>> expanded, B14, CR722 \\ >>>>> +NS CPMG 2-site star full & NS CPMG 2-site 3D full, B14 full, >>>>> CR72 full, NS CPMG 2-site 3D, NS CPMG 2-site star, \\ >>>>> + & NS CPMG 2-site expanded, B14, CR72 \\ >>>>> + >>>>> +% SQ, ZQ, DQ and MQ CPMG-type models. >>>>> +\\[-5pt] >>>>> +MMQ (SQ, ZQ, DQ, \& MQ) CPMG-type \\ >>>>> +\cline{1-1} >>>>> +MMQ CR72 & NS MMQ 2-site \\ >>>>> +NS MMQ 2-site & MMQ CR72 \\ >>>>> +NS MMQ 3-site linear & NS MMQ 2-site, MMQ CR72 \\ >>>>> +NS MMQ 3-site & NS MMQ 3-site linear, NS MMQ >>>>> 2-site, MMQ CR72 \\ >>>>> + >>>>> +% R1rho-type models. >>>>> +\clearpage >>>>> +\\[-5pt] >>>>> +$\Ronerho$-type \\ >>>>> +\cline{1-1} >>>>> +M61 & - \\ >>>>> +M61 skew & - \\ >>>>> +DPL94 & - \\ >>>>> +DPL94 $\Rone$ fit & DPL94 \\ >>>>> +TP02 & MP05, TAP03 \\ >>>>> +TP02 $\Rone$ fit & MP05 $\Rone$ fit, TAP03 $\Rone$ fit \\ >>>>> +TAP03 & MP05, TP02 \\ >>>>> +TAP03 $\Rone$ fit & MP05 $\Rone$ fit, TP02 $\Rone$ fit \\ >>>>> +MP05 & TAP03, TP02 \\ >>>>> +MP05 $\Rone$ fit & TAP03 $\Rone$ fit, TP02 $\Rone$ fit \\ >>>>> +NS $\Ronerho$ 2-site & MP05, TAP03, TP02 \\ >>>>> +NS $\Ronerho$ 2-site $\Rone$ fit & MP05 $\Rone$ fit, TAP03 $\Rone$ >>>>> fit, TP02 $\Rone$ fit \\ >>>>> +NS $\Ronerho$ 3-site linear & NS $\Ronerho$ 2-site, MP05, TAP03, >>>>> TP02 \\ >>>>> +NS $\Ronerho$ 3-site & NS $\Ronerho$ 3-site linear, NS >>>>> $\Ronerho$ 2-site, MP05, TAP03, TP02 \\ >>>>> + >>>>> +\footnotetext[1]{The nested models are ordered by preference. >>>>> +The earliest model in the list which has been optimised in the >>>>> auto-analysis will be used as the nested model. >>>>> +For example for the 'B14 full' model, the 'CR72 full' model is the >>>>> first preference, followed by 'B14', then the final fall back is >>>>> 'CR72' is neither 'CR72 full' or 'B14' have been optimised. >>>>> +If none of the nested models have been optimised, the grid search >>>>> will be performed. >>>>> +In this example, 'CR72 full' is preferred as it has perfect parameter >>>>> nesting -- all parameters of 'B14 full' are found in 'CR72 full'. >>>>> +The B14 and CR72 are fallbacks, and for these R20A and R20B are >>>>> copied from R20 so they start optimisation as R20A == R20B. >>>>> +Hence 'CR72 full' whereby R20A != R20B is a much better starting >>>>> point as R20A and R20B have been optimised to different values. >>>>> +But because of the large model instability in the 'CR72 full' model, >>>>> you may wish to instead start with 'B14'.} >>>>> + >>>>> +\end{longtable} >>>>> +\end{small} >>>>> +\end{center} >>>>> +\end{landscape} >>>>> >>>>> >>>>> % Dispersion curve insignificance. >>>>> >>>>> >>>>> _______________________________________________ >>>>> relax (http://www.nmr-relax.com) >>>>> >>>>> This is the relax-commits mailing list >>>>> relax-comm...@gna.org >>>>> >>>>> 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://www.nmr-relax.com) >>>>> >>>>> This is the relax-devel mailing list >>>>> relax-devel@gna.org >>>>> >>>>> 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://www.nmr-relax.com) This is the relax-devel mailing list relax-devel@gna.org 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
