This should now be fixed. 2014-08-20 12:21 GMT+02:00 Edward d'Auvergne <[email protected]>: > Here is another way of thinking of this optimisation problem. When > dw_AB = dw_BC and kex_AB = kex_BC, then you only have two states and > the population parameter optimised will be (pB + pC). I.e. pB and pC > will be convoluted. There are infinite values for pB and infinite > values for pC, just as long as the value of pB + pC remains the same. > This introduces lines of infinite solutions in the optimisation space. > So I don't think a grid search over pB in this situation will do > anything interesting in this situation. The dw and kex parameters > have to diverge first before pB and pC are decoupled, and the simplex > optimisation will allow that to happen. > > Regards, > > Edward > > > On 20 August 2014 09:34, Edward d'Auvergne <[email protected]> wrote: >> I'm not sure what the best behaviour would be as we don't have much to >> test against. As all the parameters will be the same for AB and BC, I >> don't think pB will change in a grid search. Or it will change but >> that pB and pC are convoluted together, as they represent the same >> state as they have the same parameter values and you have an infinite >> set of pB, pC solutions. So maybe it is best to calculate it as you >> said and hence set pC to zero to allow the two states to differentiate >> during optimisation. But I could be wrong. As long as there is a >> sentence in the auto-analysis part of the dispersion chapter of the >> manual explaining the behaviour, either might be ok. >> >> Cheers, >> >> Edward >> >> >> >> On 20 August 2014 09:27, Troels Emtekær Linnet <[email protected]> wrote: >>> I can also let it be. >>> >>> One parameter left for Grid Search should be okay. :-) >>> >>> Best >>> Troels >>> >>> 2014-08-19 18:44 GMT+02:00 Troels Emtekær Linnet <[email protected]>: >>>> 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
