I can set it 1 - pA? Best Troels
2014-08-19 18:13 GMT+02:00 Edward d'Auvergne <[email protected]>: > 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 <[email protected]> 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 <[email protected]>: >>> 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 <[email protected]> >>> 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: <[email protected]> >>>> Date: 2014-08-19 16:07 GMT+02:00 >>>> Subject: r25077 - /trunk/docs/latex/dispersion.tex >>>> To: [email protected] >>>> >>>> >>>> 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 >>>> [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://www.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://www.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
