relax SVN archive

Updated the frame order optimisation results for the CaM free rotor test data.

The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo simulations. The new
frame order representation files have been added to the repository, as well as the intermediate
state files.

Merged revisions 24535-24536 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r24535 | bugman | 2014-07-15 12:36:47 +0200 (Tue, 15 Jul 2014) | 5 lines

Created the time user function.

This is just a shortcut for printing out the output of the time.asctime() function.
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r24536 | bugman | 2014-07-15 12:38:40 +0200 (Tue, 15 Jul 2014) | 3 lines

The time user function now uses the chronometer Oxygen icon in the GUI.
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The time user function now uses the chronometer Oxygen icon in the GUI.

Created the time user function.

This is just a shortcut for printing out the output of the time.asctime() function.

Updated the frame order optimisation results for the 2nd CaM free rotor test data.

The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo simulations. The new
frame order representation files have been added to the repository, as well as the intermediate
state files.

Modified the frame_order_free_start.py script to better mimic the frame order auto-analysis.

Moved the setup of the target function data structures in the frame order analysis.

This is for the grid_search and minimise user functions. The target function data setup function
has been renamed to target_fn_data_setup(). This is now called before the Frame_order_grid_command
and Frame_order_minimise_command multi-processor objects are initialised, and all of the data is now
passed into these functions. Although the code is uglier, this has the benefit that the
target_fn_data_setup() function will only be called once. This data setup requires a lot of time,
so for a large cluster, this can be a large time saving for the grid search.

Improvements for the parallelised grid search for the frame order analysis.

As each grid point can take wildly different numbers of CPU cycles to calculate the chi-squared
value for, the result of subdividing the grid search was that some subdivisions where incredibly
quick while others required much larger amounts of time. To avoid this bad slave management, the
grid points are now randomised. This means that the subdivisions will require about the same amount
of time to optimise.

Sent the verbosity argument to the minfx.grid.grid_split() function for the frame order analysis.

This matches the relax trunk changes for the model-free analysis. The minfx function in the next
release (1.0.8) will now be more verbose, so this will help with user feedback when running the
model-free analysis on a cluster or multi-core system using MPI.

Merged revisions 24521,24526-24528 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r24521 | bugman | 2014-07-11 10:39:52 +0200 (Fri, 11 Jul 2014) | 6 lines

Updated the minfx version in the release checklist document to 1.0.8.

This version has not been released yet, but it will include important fixes and additions for
constrained parallelised grid searches.
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r24526 | bugman | 2014-07-11 16:19:49 +0200 (Fri, 11 Jul 2014) | 3 lines

Fix for a broken link in the development chapter of the relax manual.
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r24527 | bugman | 2014-07-11 16:25:35 +0200 (Fri, 11 Jul 2014) | 6 lines

Fixes for dead hyperlinks in the relaxation dispersion chapter of the relax manual.

The B14 model links to http://www.nmr-relax.com/api/3.2/lib.dispersion.b14-module.html were broken
as the B in B14 was capitalised.
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r24528 | bugman | 2014-07-11 16:43:26 +0200 (Fri, 11 Jul 2014) | 6 lines

Sent in the verbosity argument value to the minfx.grid.grid_split() function.

The minfx function in the next release (1.0.8) will now be more verbose, so this will help with user
feedback when running the model-free analysis on a cluster or multi-core system using MPI.
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