relax SVN archive

Merged revisions 25965 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r25965 | bugman | 2014-09-23 10:49:12 +0200 (Tue, 23 Sep 2014) | 8 lines

Shifted the specific_analyses.relax_disp.variables module into lib.dispersion.

This is both to minimise circular dependencies, as previously the specific_analyses.relax_disp
modules import from target_functions.relax_disp and vice-versa, and to allow the relax library
functions to have access to these variables. This follows from a similar change to the frame order
analysis in the frame_order_cleanup branch.
........

Shifted the specific_analyses.relax_disp.variables module into lib.dispersion.

This is both to minimise circular dependencies, as previously the specific_analyses.relax_disp
modules import from target_functions.relax_disp and vice-versa, and to allow the relax library
functions to have access to these variables. This follows from a similar change to the frame order
analysis in the frame_order_cleanup branch.

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.
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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.