relax SVN archive

Modified the populations.py N-state model system test script to better test optimisation.

The probability of the 2nd state has been slightly shifted to make sure the original value can be
found.

Improved the comments in the _disassemble_param_vector() N-state model method.

Simplified the parameter unpacking in the func_standard() N-state model target function.

Merged revisions 18275,18277 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r18275 | bugman | 2013-01-23 17:39:04 +0100 (Wed, 23 Jan 2013) | 3 lines

Removed a duplicated comment.
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r18277 | bugman | 2013-01-23 18:14:33 +0100 (Wed, 23 Jan 2013) | 6 lines

BFGS optimisation is now being used for the N_state_model.test_mc_sim_failure system test.

This is to have better test coverage of the paramagnetic centre position optimisation gradient code
paths.
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BFGS optimisation is now being used for the N_state_model.test_mc_sim_failure system test.

This is to have better test coverage of the paramagnetic centre position optimisation gradient code
paths.

Merged revisions 18260-18274 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r18260 | bugman | 2013-01-22 20:13:33 +0100 (Tue, 22 Jan 2013) | 12 lines

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).
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r18261 | bugman | 2013-01-22 21:47:41 +0100 (Tue, 22 Jan 2013) | 3 lines

Added some more checks to the metal_pos_opt.py N-state model system test script.
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r18262 | bugman | 2013-01-22 23:07:02 +0100 (Tue, 22 Jan 2013) | 10 lines

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.
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r18263 | bugman | 2013-01-23 10:49:15 +0100 (Wed, 23 Jan 2013) | 9 lines

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.
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r18264 | bugman | 2013-01-23 10:50:15 +0100 (Wed, 23 Jan 2013) | 3 lines

Removed the unused parameter scaling in the N-state model gradient and Hessian target functions.
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r18265 | bugman | 2013-01-23 11:08:10 +0100 (Wed, 23 Jan 2013) | 5 lines

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.
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r18266 | bugman | 2013-01-23 11:21:27 +0100 (Wed, 23 Jan 2013) | 5 lines

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.
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r18267 | bugman | 2013-01-23 16:09:34 +0100 (Wed, 23 Jan 2013) | 5 lines

Expanded the N-state model target function func_standard() docstring to include the xi derivative.

This is the partial derivative with respect to the paramagnetic centre position.
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r18268 | bugman | 2013-01-23 16:10:21 +0100 (Wed, 23 Jan 2013) | 3 lines

Bug fix for the N-state model target functions - now copies of the gradient and Hessian are returned.
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r18269 | bugman | 2013-01-23 16:11:51 +0100 (Wed, 23 Jan 2013) | 5 lines

Bug fix for the N-state model optimisation of populations and paramagnetic position.

The gradient from dfunc_standard() is now correctly calculated when both are optimised.
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r18270 | bugman | 2013-01-23 16:15:15 +0100 (Wed, 23 Jan 2013) | 3 lines

Comment fixes in the ave_pcs_tensor_ddeltaij_dc() and pcs_constant_grad() functions.
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r18271 | bugman | 2013-01-23 16:16:39 +0100 (Wed, 23 Jan 2013) | 6 lines

Bug fix for the calculation of the PCS gradient with respect to the paramagnetic coordinates.

This is in the ave_pcs_tensor_ddeltaij_dc() function - the gradient needs to be converted back to
the Angstrom units of the paramagnetic position parameters.
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r18272 | bugman | 2013-01-23 16:22:53 +0100 (Wed, 23 Jan 2013) | 5 lines

Constraints are now allowed for the paramagnetic position optimisation in the N-state model.

This is because the gradients are implemented and functional.
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r18273 | bugman | 2013-01-23 16:34:03 +0100 (Wed, 23 Jan 2013) | 6 lines

Fix for the assembly of the N-state model linear constraints.

These were not set up correctly when the populations and paramagnetic position are optimised
together.
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r18274 | bugman | 2013-01-23 16:48:37 +0100 (Wed, 23 Jan 2013) | 5 lines

Modified the N-state model metal_pos_opt.py system test script.

This is to test optimisation with the new paramagnetic position gradients.
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Removed a duplicated comment.

Modified the N-state model metal_pos_opt.py system test script.

This is to test optimisation with the new paramagnetic position gradients.

Fix for the assembly of the N-state model linear constraints.

These were not set up correctly when the populations and paramagnetic position are optimised
together.

Constraints are now allowed for the paramagnetic position optimisation in the N-state model.

This is because the gradients are implemented and functional.