relax SVN archive

Created a master profiling script for comparing the speed between different dispersion models.

This is similar to the disp_profile_all.py script except it only operates on a single relax version.
The output is then simply the timings, with statistics, of the calculation time for 100 function
calls for 100 spins (either 10,000 function calls for single spins or 100 function calls for the
cluster of 100 spins).

The output of the script for the current disp_spin_speed branch code has also been added.

Added better epydoc sectioning to the lib.dispersion.ns_cpmg_2site_expanded module docstring.

This is to better separate the original scripts used to document the code evolution.

A very small speed up to the MMQ CR72 dispersion model by minimising repetitive maths operations.

This matches the recent change for the CR72 model (r24353), though the Psi calculation was already
using the fast form. Using the disp_profile_all.py script, the speed ups are:

100 single spins analysis:
MMQ CR72: 4.276+/-0.066 -> 4.230+/-0.089, 1.011x faster.

Cluster of 100 spins analysis:
MMQ CR72: 0.883+/-0.015 -> 0.862+/-0.010, 1.024x faster.

Merged revisions 24354-24355 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r24354 | bugman | 2014-06-27 18:13:27 +0200 (Fri, 27 Jun 2014) | 16 lines

Numpy version 1.6 or higher is now required to be able to run relax.

This follows from the series of messages:

- http://www.mail-archive.com/relax-devel@.../msg06288.html,
- http://www.mail-archive.com/relax-devel@.../msg06289.html,
- http://www.mail-archive.com/relax-devel@.../msg06327.html,
- http://www.mail-archive.com/relax-devel@.../msg06335.html.

If too many users complain, maybe this change can be reverted later. This minimal numpy version is
needed for many of the speed ups going in the relaxation dispersion and frame order analyses. It is
required for the numpy ufunc out arguments and for the numpy.eigsum() function. These will likely
be used in other analyses in the future for improving the speed of relax, so it might affect users
of other analyses later on.
........
r24355 | bugman | 2014-06-27 18:14:26 +0200 (Fri, 27 Jun 2014) | 3 lines

Updated the numpy minimal dependency in the installation chapter of the manual to version 1.6.
........

Removed unused imports.

This is from the splitting of the specific_analyses.frame_order.uf module into the new geometric
module.

Removal of a tonne of unused imports in the lib.dispersion package.

These were identified using the command "pylint * --disable=all --enable=unused-import".

Updated the numpy version requirement to be >= 1.6 on the http://www.nmr-relax.com/download.html webpage.

Updated the numpy minimal dependency in the installation chapter of the manual to version 1.6.

Numpy version 1.6 or higher is now required to be able to run relax.

This follows from the series of messages:

- http://www.mail-archive.com/relax-devel@.../msg06288.html,
- http://www.mail-archive.com/relax-devel@.../msg06289.html,
- http://www.mail-archive.com/relax-devel@.../msg06327.html,
- http://www.mail-archive.com/relax-devel@.../msg06335.html.

If too many users complain, maybe this change can be reverted later. This minimal numpy version is
needed for many of the speed ups going in the relaxation dispersion and frame order analyses. It is
required for the numpy ufunc out arguments and for the numpy.eigsum() function. These will likely
be used in other analyses in the future for improving the speed of relax, so it might affect users
of other analyses later on.

A very small speed up to the CR72 dispersion models by minimising repetitive maths operations.

The k_BA and k_AB rates are used to simplify the Psi calculation, dropping from 3 to 2
multiplications and removing a squaring operation. The Dpos and Dneg value calculations have been
simplified to drop one multiplication operation. And the calculation of eta_scale / cpmg_frqs now
only occurs once rather than twice.

Using the disp_profile_all.py script, the speed ups for these two models are:

100 single spins analysis:
CR72: 1.608+/-0.025 -> 1.552+/-0.028, 1.036x faster.
CR72 full: 1.795+/-0.043 -> 1.705+/-0.024, 1.053x faster.

Cluster of 100 spins analysis:
CR72: 0.109+/-0.001 -> 0.107+/-0.001, 1.026x faster.
CR72 full: 0.114+/-0.004 -> 0.110+/-0.001, 1.034x faster.