relax SVN archive

The N_state_model.test_align_fit system test now checks the simulation PCS values.

Merged revisions 18289-18295 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r18289 | bugman | 2013-01-24 10:02:33 +0100 (Thu, 24 Jan 2013) | 5 lines

Added Monte Carlo simulations to the align_fit.py N-state model system test script.

This is to increase the very low coverage of Monte Carlo simulation testing for the N-state model.
........
r18290 | bugman | 2013-01-24 10:56:29 +0100 (Thu, 24 Jan 2013) | 6 lines

Modified the metal_pos_opt.py N-state model system test script to test the bootstrapping code path.

This converts the Monte Carlo simulations into bootstrapping to make sure this method also
functions correctly.
........
r18291 | bugman | 2013-01-24 10:57:51 +0100 (Thu, 24 Jan 2013) | 5 lines

Implemented the N-state model specific return_data() method.

This is needed for bootstrapping.
........
r18292 | bugman | 2013-01-24 11:05:38 +0100 (Thu, 24 Jan 2013) | 3 lines

Fixes for the N-state model return_data() method.
........
r18293 | bugman | 2013-01-24 11:22:02 +0100 (Thu, 24 Jan 2013) | 5 lines

Modified the RelaxNoRDCError and RelaxNoPCSError to accept no alignment ID.

This is then used to indicate the complete absence of data.
........
r18294 | bugman | 2013-01-24 11:23:12 +0100 (Thu, 24 Jan 2013) | 5 lines

Modified the initial testing of the rdc.set_errors and pcs.set_errors user functions.

This is to better indicate to the user what the problem is and why the user function cannot operate.
........
r18295 | bugman | 2013-01-24 11:25:17 +0100 (Thu, 24 Jan 2013) | 7 lines

Fixes for the align_fit.py N-state model system test script.

The recently introduced Monte Carlo simulations and associated RDC and PCS error setting was failing
when RDC or PCS data was missing. The script now checks the mode of operation and only sets errors
if the corresponding data is present.
........

Fixes for the align_fit.py N-state model system test script.

The recently introduced Monte Carlo simulations and associated RDC and PCS error setting was failing
when RDC or PCS data was missing. The script now checks the mode of operation and only sets errors
if the corresponding data is present.

Modified the initial testing of the rdc.set_errors and pcs.set_errors user functions.

This is to better indicate to the user what the problem is and why the user function cannot operate.

Modified the RelaxNoRDCError and RelaxNoPCSError to accept no alignment ID.

This is then used to indicate the complete absence of data.

Fixes for the N-state model return_data() method.

Implemented the N-state model specific return_data() method.

This is needed for bootstrapping.

Modified the metal_pos_opt.py N-state model system test script to test the bootstrapping code path.

This converts the Monte Carlo simulations into bootstrapping to make sure this method also
functions correctly.

Added Monte Carlo simulations to the align_fit.py N-state model system test script.

This is to increase the very low coverage of Monte Carlo simulation testing for the N-state model.

Merged revisions 18279-18287 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r18279 | bugman | 2013-01-23 18:51:33 +0100 (Wed, 23 Jan 2013) | 3 lines

Simplified the parameter unpacking in the func_standard() N-state model target function.
........
r18280 | bugman | 2013-01-23 21:08:23 +0100 (Wed, 23 Jan 2013) | 3 lines

Improved the comments in the _disassemble_param_vector() N-state model method.
........
r18281 | bugman | 2013-01-23 21:09:49 +0100 (Wed, 23 Jan 2013) | 6 lines

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.
........
r18282 | bugman | 2013-01-23 21:35:53 +0100 (Wed, 23 Jan 2013) | 5 lines

Bug fix for the N-state model Hessian d2func_standard() method.

An index variable name was incorrect causing the population model to fail with Newton optimisation.
........
r18283 | bugman | 2013-01-23 21:38:05 +0100 (Wed, 23 Jan 2013) | 5 lines

Modified the metal_pos_opt.py N-state model system test script to demonstrate some failures.

This change also caught the bug fixed in r18282.
........
r18284 | bugman | 2013-01-23 21:41:08 +0100 (Wed, 23 Jan 2013) | 3 lines

Improved the checks of the metal_pos_opt.py N-state model system test script.
........
r18285 | bugman | 2013-01-23 22:12:42 +0100 (Wed, 23 Jan 2013) | 5 lines

Bug fixes for the _opt_uses_pcs() and _opt_uses_rdc() N-state model methods.

These now check that the populations are optimised as well.
........
r18286 | bugman | 2013-01-23 22:14:19 +0100 (Wed, 23 Jan 2013) | 3 lines

Modified the metal_pos_opt.py N-state model system test script to catch yet another bug.
........
r18287 | bugman | 2013-01-23 22:51:13 +0100 (Wed, 23 Jan 2013) | 6 lines

Fix for a bug caught by the N_state_model.test_metal_pos_opt system test.

The problem was that uninitalised probability arrays of None from cdp.probs was always sent into the
target function, whereas None should be sent in instead.
........