relax SVN archive

Created a special internal structural object selection object.

This will be used for massively speeding up the internal structural object. The use of the
lib.selection module by the internal structural object is currently very slow as a huge number of
calls to re.search() are required. The idea is to avoid this by using lib.selection once to
populate this new selection object, and then reusing this object to loop over molecules and atoms.

Implemented the frame_order.simulate user function backend for the double rotor frame order model.

This involved extending the algorithm to loop over N states, where N=2 for the double rotor and N=1
for all other models. To handle the rotations being about the x and y-axes, an axis permutation
algorithm is used to shift these axes to z prior to decomposing to the torsion-tilt angles. The
reverse permutation is used to shift the axes back after correcting for being outside of the allowed
angles.

Merged revisions 25967-25968 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r25967 | bugman | 2014-09-23 13:59:05 +0200 (Tue, 23 Sep 2014) | 6 lines

Dependency fix for the auto_analyses.relax_disp_repeat_cpmg module.

This was causing relax to fail. SciPy is an optional dependence for relax, but this module caused
relax to not start if scipy was not installed. This was detected by testing relax with PyPy.
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r25968 | tlinnet | 2014-09-23 14:41:49 +0200 (Tue, 23 Sep 2014) | 3 lines

Implemented writing out of particular correlation plots to file.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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Implemented writing out of particular correlation plots to file.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.

Dependency fix for the auto_analyses.relax_disp_repeat_cpmg module.

This was causing relax to fail. SciPy is an optional dependence for relax, but this module caused
relax to not start if scipy was not installed. This was detected by testing relax with PyPy.

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

........
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).