relax SVN archive

Clean up of some of the logic in N-state model analysis specific code.

The following methods have been added:
_opt_tensor(),
_opt_uses_align_data(),
_opt_uses_pcs(),
_opt_uses_rdc()

These are used through the class to determine what is needed for or used during optimisation,
making a lot of checking code more consistent (hence removing latent bugs).

Merged revisions 18249-18258 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r18249 | bugman | 2013-01-21 21:30:10 +0100 (Mon, 21 Jan 2013) | 5 lines

Modified the N_state_model.test_mc_sim_failure to demonstrate a failure in paramagnetic centre code.

The failure is for the combination of paramagnetic centre optimisation and Monte Carlo simulations.
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r18250 | bugman | 2013-01-21 21:33:40 +0100 (Mon, 21 Jan 2013) | 5 lines

Fix for the N-state model _minimise_setup_atomic_pos() method for the paramagnetic centre.

The cdp.paramagnetic_centre_sim may not exist prior to Monte Carlo simulations.
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r18251 | bugman | 2013-01-21 21:36:42 +0100 (Mon, 21 Jan 2013) | 3 lines

Modified the paramag.centre user function printouts for the 'fix' flag.
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r18252 | bugman | 2013-01-21 21:37:08 +0100 (Mon, 21 Jan 2013) | 3 lines

Fix for the recent changes to the N_state_model.test_mc_sim_failure system test.
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r18253 | bugman | 2013-01-21 21:41:29 +0100 (Mon, 21 Jan 2013) | 6 lines

The alignment tensor objects in the relax data store now support sequential Monte Carlo analyses.

The AlignTensorData.set_sim_num() method was preventing a second Monte Carlo error analysis from
being performed by throwing a RelaxError. The check for previous simulations has been killed.
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r18254 | bugman | 2013-01-21 22:37:54 +0100 (Mon, 21 Jan 2013) | 5 lines

Fix for the Monte Carlo initialisation of the paramagnetic centre position in the N-state model.

The simulation positions are now initialised to the optimised position.
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r18255 | bugman | 2013-01-21 23:37:09 +0100 (Mon, 21 Jan 2013) | 3 lines

Fix for the N-state model Monte Carlo simulations for when the paramagnetic centre is fixed.
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r18256 | bugman | 2013-01-22 09:56:39 +0100 (Tue, 22 Jan 2013) | 6 lines

Added checks to the N-state model for the paramagnetic centre optimisation.

Only simplex optimisation without constraints is allowed for the paramagnetic centre position as the
PCS gradients and Hessians are not yet implemented for the coordinate parameters.
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r18257 | bugman | 2013-01-22 10:32:14 +0100 (Tue, 22 Jan 2013) | 6 lines

Improved the RDC and PCS Q factor calculation warnings to be more informative.

These warnings sometimes appear at the end of the N-state model optimisation, but it is not clear
where they come from.
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r18258 | bugman | 2013-01-22 11:11:01 +0100 (Tue, 22 Jan 2013) | 5 lines

Fix for a recently introduced breakage of the N_state_model.test_mc_sim_failure system test.

Newton optimisation is now not allowed for optimising the paramagnetic centre position.
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Fix for a recently introduced breakage of the N_state_model.test_mc_sim_failure system test.

Newton optimisation is now not allowed for optimising the paramagnetic centre position.

Improved the RDC and PCS Q factor calculation warnings to be more informative.

These warnings sometimes appear at the end of the N-state model optimisation, but it is not clear
where they come from.

Added checks to the N-state model for the paramagnetic centre optimisation.

Only simplex optimisation without constraints is allowed for the paramagnetic centre position as the
PCS gradients and Hessians are not yet implemented for the coordinate parameters.

Fix for the N-state model Monte Carlo simulations for when the paramagnetic centre is fixed.

Fix for the Monte Carlo initialisation of the paramagnetic centre position in the N-state model.

The simulation positions are now initialised to the optimised position.

The alignment tensor objects in the relax data store now support sequential Monte Carlo analyses.

The AlignTensorData.set_sim_num() method was preventing a second Monte Carlo error analysis from
being performed by throwing a RelaxError. The check for previous simulations has been killed.

Fix for the recent changes to the N_state_model.test_mc_sim_failure system test.

Modified the paramag.centre user function printouts for the 'fix' flag.