relax SVN archive

Fix for the structure.load_spins user function when the from_mols argument is used.

The load_spins_multi_mol() function of the pipe_control.structure.main module was incorrectly
handling the atomic position returned by the internal structural object atom_loop() method. This
position is a list of lists when multiple models are present. But when only a single model is
present, it returns a simple list.

Fix for the checks in the new Structure.test_load_spins_multi_mol system test.

A spin index was incorrect.

Created the Structure.test_bug_22860_CoM_after_deletion system test.

This is to catch bug #22860 (https://gna.org/bugs/?22860), the failure of the structure.com user
function after calling structure.delete.

Updated the frame order analysis for the structure.load_spins user function changes.

The minimise_setup_atomic_pos() function of the specific_analyses.frame_order.optimisation module
now handles the mixed type spin.pos variable correctly.

Merged revisions 26354-26355,26358-26362 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26354 | bugman | 2014-10-22 15:38:23 +0200 (Wed, 22 Oct 2014) | 6 lines

Changed the spin_selection argument default in the interatom.define user function backend.

This now defaults to False to allow other parts of relax which call this function to operate as
previously. The default for the interatom.define user function is however still True.
........
r26355 | bugman | 2014-10-22 15:39:47 +0200 (Wed, 22 Oct 2014) | 6 lines

Modified the Structure.test_load_spins_multi_mol system test for the spin.pos variable changes.

The atomic position for an ensemble of structures is now set to None rather than being missing, so
the system test has been updated to check for this.
........
r26358 | bugman | 2014-10-22 15:55:46 +0200 (Wed, 22 Oct 2014) | 6 lines

The align_tensor.display user function now has more consistent section formatting.

The section() and subsection() functions of the lib.text.sectioning module are now being used to
standardise these custom printouts with the rest of relax.
........
r26359 | bugman | 2014-10-22 16:22:26 +0200 (Wed, 22 Oct 2014) | 8 lines

Modifications to the new N_state_model.test_CaM_IQ_tensor_fit system test.

The system test now checks all of the optimised values to make sure the correct values have been
found. That will block any future regressions in this N-state model code path. The system test is
now also faster. And the pcs.structural_noise user function RMSD value has been set to 0.0 so that
the test no longer has a random component affecting the final optimised values.
........
r26360 | bugman | 2014-10-22 16:31:04 +0200 (Wed, 22 Oct 2014) | 6 lines

Added printouts for the rdc.calc_q_factors and pcs_calc_q_factors user functions.

These are activated by the new verbosity user function argument which defaults to 1. If the value
is greater than 0, then the backend will print out all the calculated Q factors.
........
r26361 | bugman | 2014-10-22 16:31:56 +0200 (Wed, 22 Oct 2014) | 3 lines

Small change which should have been part of the last commit (r26360).
........
r26362 | bugman | 2014-10-22 16:34:16 +0200 (Wed, 22 Oct 2014) | 5 lines

The verbosity argument of the RDC and PCS q_factors() functions now defaults to 1.

This causes the Q factors to be printed out at the end of all N-state model optimisations.
........

Merged revisions 26354-26355,26358-26362 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r26354 | bugman | 2014-10-22 15:38:23 +0200 (Wed, 22 Oct 2014) | 6 lines

Changed the spin_selection argument default in the interatom.define user function backend.

This now defaults to False to allow other parts of relax which call this function to operate as
previously. The default for the interatom.define user function is however still True.
........
r26355 | bugman | 2014-10-22 15:39:47 +0200 (Wed, 22 Oct 2014) | 6 lines

Modified the Structure.test_load_spins_multi_mol system test for the spin.pos variable changes.

The atomic position for an ensemble of structures is now set to None rather than being missing, so
the system test has been updated to check for this.
........
r26358 | bugman | 2014-10-22 15:55:46 +0200 (Wed, 22 Oct 2014) | 6 lines

The align_tensor.display user function now has more consistent section formatting.

The section() and subsection() functions of the lib.text.sectioning module are now being used to
standardise these custom printouts with the rest of relax.
........
r26359 | bugman | 2014-10-22 16:22:26 +0200 (Wed, 22 Oct 2014) | 8 lines

Modifications to the new N_state_model.test_CaM_IQ_tensor_fit system test.

The system test now checks all of the optimised values to make sure the correct values have been
found. That will block any future regressions in this N-state model code path. The system test is
now also faster. And the pcs.structural_noise user function RMSD value has been set to 0.0 so that
the test no longer has a random component affecting the final optimised values.
........
r26360 | bugman | 2014-10-22 16:31:04 +0200 (Wed, 22 Oct 2014) | 6 lines

Added printouts for the rdc.calc_q_factors and pcs_calc_q_factors user functions.

These are activated by the new verbosity user function argument which defaults to 1. If the value
is greater than 0, then the backend will print out all the calculated Q factors.
........
r26361 | bugman | 2014-10-22 16:31:56 +0200 (Wed, 22 Oct 2014) | 3 lines

Small change which should have been part of the last commit (r26360).
........
r26362 | bugman | 2014-10-22 16:34:16 +0200 (Wed, 22 Oct 2014) | 5 lines

The verbosity argument of the RDC and PCS q_factors() functions now defaults to 1.

This causes the Q factors to be printed out at the end of all N-state model optimisations.
........

The verbosity argument of the RDC and PCS q_factors() functions now defaults to 1.

This causes the Q factors to be printed out at the end of all N-state model optimisations.

Small change which should have been part of the last commit (r26360).

Added printouts for the rdc.calc_q_factors and pcs_calc_q_factors user functions.

These are activated by the new verbosity user function argument which defaults to 1. If the value
is greater than 0, then the backend will print out all the calculated Q factors.

Modifications to the new N_state_model.test_CaM_IQ_tensor_fit system test.

The system test now checks all of the optimised values to make sure the correct values have been
found. That will block any future regressions in this N-state model code path. The system test is
now also faster. And the pcs.structural_noise user function RMSD value has been set to 0.0 so that
the test no longer has a random component affecting the final optimised values.