relax SVN archive

Shifted the specific_analyses.frame_order.variables module into lib.frame_order.

This is both to minimise circular dependencies, as previously the specific_analyses.frame_order
modules import from target_functions.frame_order and vice-versa, and to allow the relax library
functions to have access to these variables.

Merged revisions 25962 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r25962 | bugman | 2014-09-23 10:00:21 +0200 (Tue, 23 Sep 2014) | 8 lines

Updated the minimum minfx dependency version number from 1.0.9 to 1.0.11 in the dep_check module.

This newest version handles infinite target function values preventing optimisation from continuing
forever (https://gna.org/forum/forum.php?forum_id=2477). The 1.0.10 version is also useful as there
is full support for gradients and Hessians in the log-barrier constraint algorithm
(https://gna.org/forum/forum.php?forum_id=2475).
........

Updated the minimum minfx dependency version number from 1.0.9 to 1.0.11 in the dep_check module.

This newest version handles infinite target function values preventing optimisation from continuing
forever (https://gna.org/forum/forum.php?forum_id=2477). The 1.0.10 version is also useful as there
is full support for gradients and Hessians in the log-barrier constraint algorithm
(https://gna.org/forum/forum.php?forum_id=2475).

Implemented the pseudo-Brownian frame order dynamics simulation for the single motion models.

This uses the same logic as in the test_suite/shared_data/frame_order/cam/*/generate_distribution.py
scripts which were used to generate all of the test suite data. However rather than using a random
rotation matrix, a random 3D vector is used to rotate a fixed angle. And the rotation is used to
rotate the current state to state i+1. The rotation for the state is decomposed into torsion-tilt
angles once shifted into the motional eigenframe, the violations checked for as the state shifted to
the boundary, then the new state reconstructed from the corrected torsion-tilt angles, and then it
is shifted from the motional eigenframe to the PDB frame.

Fix for the new specific_analyses.frame_order.geometric.generate_axis_system() function.

The rotor and free rotor models were not correctly handled and the returned eigenframe was the zero
matrix.

Merged revisions 25947,25957-25958 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r25947 | bugman | 2014-09-22 11:15:17 +0200 (Mon, 22 Sep 2014) | 5 lines

Created a basic text based progress meter in the new lib.text.progress module.

This is taken from the script test_suite/shared_data/frame_order/cam/generate_base.py.
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r25957 | bugman | 2014-09-22 16:43:38 +0200 (Mon, 22 Sep 2014) | 6 lines

Modifications to the User_functions.test_structure_add_atom GUI test.

As lists of lists are now accepted by the structure.add_atom user function, the operation in the GUI
is now significantly different. Therefore many checks have been removed from the GUI test.
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r25958 | bugman | 2014-09-22 16:44:57 +0200 (Mon, 22 Sep 2014) | 6 lines

Added safety checks for NaN values to the lib.structure.pdb_write module.

This is within the _record_validate() function. The check prevents the creation of invalid PDB
files.
........

Added safety checks for NaN values to the lib.structure.pdb_write module.

This is within the _record_validate() function. The check prevents the creation of invalid PDB
files.

Modifications to the User_functions.test_structure_add_atom GUI test.

As lists of lists are now accepted by the structure.add_atom user function, the operation in the GUI
is now significantly different. Therefore many checks have been removed from the GUI test.

Created the specific_analyses.frame_order.geometric.generate_axis_system() function.

This is now used by most parts of the frame order analysis to generate the full 3D eigenframe of the
motions. Previously this was implemented each time the frame or major axis was required. This
replicated and highly inconsistent code has been eliminated.

Changed the default PDB file name for the frame_order.simulate user function to 'simulate.pdb'.

The '*.bz2' extension has been dropped so that the file is quicker to create and does not need to be
decompressed for loading into molecular viewers.