relax SVN archive

Implementation of the Optimisation_settings object in the frame order auto-analysis.

This object holds all of the grid search, zooming grid search, and minimisation settings. It
provides the add_grid() and add_min() methods to allow the user to add successive iterations of
optimisation and settings to the object. The loop_grid() and loop_min() methods are used to loop
over each iteration of each method. And the get_grid_inc(), get_grid_num_int_pts(),
get_grid_zoom_level(), get_min_algor(), get_min_func_tol() and get_min_num_int_pts() methods are
used to access the user defined settings.

The auto-analysis has been redesigned around this new concept. All of the optimisation arguments
have been replaced. Instead there are the opt_rigid, opt_subset, opt_full, and opt_mc arguments
which are expected to be instances of the Optimisation_settings object. The optimisation in the
auto-analysis is now more advanced in that more user optimisation settings are now available and
active.

Redesigned the Frame_order.test_auto_analysis system test.

This now uses a hypothetical new Optimisation_settings object from the frame order auto-analysis
module for holding all of the grid search, zooming grid search and minimisation settings. This will
allow for far greater user control of the settings and hugely simplify the auto-analysis interface
by decreasing the number of input arguments. It should also be less confusing.

Updates and fixes for the frame order auto-analysis.

The custom grid setup now works for the new reduced parameter set models and the double rotor model
is now also included. The cone axis alpha angle to spherical angle conversion has had a bug
removed. And some of the printouts are now more detailed.

Missing import in the lib.frame_order.double_rotor module.

This was identified by the new Frame_order.test_auto_analysis system test.

Merged revisions 24788,24796-24797 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r24788 | bugman | 2014-07-29 10:11:14 +0200 (Tue, 29 Jul 2014) | 9 lines

Implemented the pipe_control.mol_res_spin.format_info_full() function.

This follows from http://thread.gmane.org/gmane.science.nmr.relax.scm/22522/focus=6534.

This is a verbose representation of the spin information which can be used for presenting to the
user. Functions for shorter string versions will also be of great use, for example as described by
Troels at http://thread.gmane.org/gmane.science.nmr.relax.scm/22522/focus=6535.
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r24796 | bugman | 2014-07-29 10:25:37 +0200 (Tue, 29 Jul 2014) | 3 lines

Fix for the pipe_control.mol_res_spin.format_info_full() function, it now actually returns the string.
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r24797 | bugman | 2014-07-29 10:51:20 +0200 (Tue, 29 Jul 2014) | 5 lines

Created a unit test for the pipe_control.mol_res_spin.format_info_full() function.

This comprehensive test covers all input argument combinations.
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Missing import in the lib.frame_order.rotor module.

This was identified by the new Frame_order.test_auto_analysis system test.

Modified the optimisation of the rigid model in the frame order auto-analysis.

The grid search is now implemented as a zooming grid search.

Fixes for all of the Frame_order.test_rigid_data_to_*_model system tests.

The base script now sets all parameter values so that the minimise.calculate user function can
operate. The two free rotor model chi-squared values have been updated as these are sensitive to
the motional eigenframe parameter values - these models can never approximate a rigid state.

Better handling of unset parameters in the frame order optimisation functions.

The specific_analyses.frame_order.optimisation.target_fn_data_setup() and
specific_analyses.frame_order.parameters.assemble_param_vector() function both now accept the
unset_fail argument. This is set in both the calculate() and minimise() API methods. When set, a
RelaxError will be raised in the assemble_param_vector() function when a parameter has not been set
yet. This together with previous changes will prevent the frame order analysis from using 0.0 as a
starting value for unset parameters.

Renamed the other return grace data function, to a better shorter name.

sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].