Hi, If you look into the specific_analyses.relax_disp.parameters.linear_constraints() function, you should see why kA can go negative. You will notice other places in this module where kA is not correctly handled. But before you make these changes, we should change kA to k_AB everywhere! This is to make the notation consistent within relax. Actually, ka can be used in the lib.dispersion module, but in all other parts of relax it needs to be k_AB. kA is ambiguous and inconsistent with the other models in relax.
Regards, Edward On 4 September 2013 13:51, Troels Emtekær Linnet <[email protected]> wrote: > Well. > > Most of my values for kA are 2-6. > Which seems fine. > > But I also got a negative kA value and one of thousands. > And my dw values are also strange. > > I have to look into which units the paper report data in, and > if there are more supporting information I can look at. > > Let me return to this, when I have setup a test-suite. > > Best > Troels > > Troels Emtekær Linnet > > > 2013/9/4 Edward d'Auvergne <[email protected]>: >> Hi, >> >>> Is there a way to see the start value for a variable in a CPMG model fit. ? >> >> Not in the auto-analysis, as there are no starting values. >> >> >>> When using the auto_analysis, : >>> >>> -------- >>> from auto_analyses.relax_disp import Relax_disp >>> Relax_disp(pipe_name=pipe_name, pipe_bundle=pipe_bundle, >>> results_dir=results_directory, models=MODELS, grid_inc=GRID_INC, >>> mc_sim_num=MC_NUM, modsel=MODSEL) >>> -------- >>> >>> I see no options to modify the grid_search ? >> >> Currently the only option is to change the number of grid increments. >> For the auto-analysis, changing the other options is not such a good >> idea. For a custom dispersion analysis, you are free to do anything. >> The auto-analysis is limited to help users who are only interested in >> a result whereas a custom analysis is unlimited in what can be done. >> Actually if the user changes the grid increments to be below 7, that >> could be fatal for the results. The defaults in relax must allow the >> minimum to be found in absolutely all cases, and the current defaults >> should do that. >> >> >>> When I grep the logfile, I see each model use a grid_search >>> >>> grid_search(lower=None, upper=None, inc=21, constraints=True, verbosity=1) >>> http://www.nmr-relax.com/api/3.0/pipe_control.minimise-module.html#grid_search >>> >>> Is it possible change the lower and upper bonds for the grid_search, >>> or should one run all the commands manually? >> >> These cannot be changed in the auto-analysis. The reason for this is >> that relax provides defaults which will work in all cases. To see >> this, look at the _grid_search_setup() method in the >> specific_analyses.relax_disp.api module. The user should really not >> touch these upper and lower bounds as they might cause the minimum to >> be missed. A power user not using the auto-analysis can play with >> such things, but definitely not a normal user. However a power user >> should probably not change these anyway. >> >> Note that the constraints will remove half of this grid due to the pA >>> pB constraint. The other constraints remove other parts of the >> grid. But the grid is only used to find a rough starting point for >> optimisation so that the minimiser can easily find the minimum. This >> is not a question of local verses global minima, as there is only one >> minimum for the 2-site models (analytic and numeric). The problem is >> that if you start too far from the minimum, due to the non-linearity >> of the parameter space the optimisation algorithm may not be able to >> reach the minimum. This is why a grid search is almost always used as >> the starting point for mathematical optimisation. There are other >> techniques that can be used, but they are similar in concept - you >> simply need some algorithm pick a rough position close to the minimum. >> Then you use the optimisation algorithm to refine and find the exact >> values. >> >> So you start with no parameter values, use the grid search to find a >> rough starting position, then use the simplex optimisation algorithm >> to refine the parameter values. The rough parameter values after the >> grid search are of no scientific interest, so these numbers are never >> output (apart from the printouts from the grid search itself). The >> values are stored in relax to be used by the subsequent minimise() >> user function, and then they are overwritten by the higher precision >> parameters. >> >> >>> I could grep the logfile after an Autoanalysis to see the commands: >>> http://wiki.nmr-relax.com/Grep_log_file >>> and then change the grid search parameters. >> >> What is the purpose of changing these? Are the defaults not good enough? >> >> >>> --- >>> On another note. >>> >>> Would it be possible to write the starting values into the table 10.1 >>> in the relax_disp >>> manual? >> >> No, because there is no such thing as a starting value ;) >> >> Regards, >> >> Edward > > _______________________________________________ > 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
