relax SVN archive

The probabilities and paramagnetic position can now be simultaneously in the N-state model.

Such a combination would have previously failed to unpack the parameters correctly.

Added a RelaxError to the N-state model Hessian for the optimisation of the paramagnetic position.

This is because these equations are not derived or coded yet.

Removed the unused parameter scaling in the N-state model gradient and Hessian target functions.

Major code simplification of the N-state model target functions.

The func_tensor_opt(), dfunc_tensor_opt(), and d2func_tensor_opt() methods have been merged with the
func_population(), dfunc_population(), and d2func_population() methods into the new func_standard(),
dfunc_standard(), and d2func_standard() methods. This halves the amount of code required to be
maintained and debugged. For the merger, the new probs_fixed class instance variable has been
created to determine when the probabilities need to be unpacked from the parameter vector.

First attempt at implementing the paramagnetic centre position gradient in the N-state model.

This will be used for faster optimisation of the lanthanide position. Two new functions have been
added:
maths_fns.pcs.ave_pcs_tensor_ddeltaij_dc()
maths_fns.pcs.pcs_constant_grad()

These are used by the dfunc_*() methods of the N-state model target function class.

Added some more checks to the metal_pos_opt.py N-state model system test script.

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.