relax SVN archive

Added support for the isotopic cone models to the frame_order.permute_axes user function.

This is a simpler setup, but it uses the same permutation algorithm as derived for the
pseudo-ellipse models. Instead of setting the x and y cone angles separately, they are instead
averaged. And as the cone axis is undefined in the xy plane, the axis has been randomly selected as
being the axis perpendicular to both the z-axis and the reference frame x-axis.

Visualisation files for all of the pseudo-ellipse permutations by frame_order.permute_axes.

This includes the x <= z <= y and z <= x <= y conditions (the previous files were for x <= y <= z).
In all permutation combinations, optimisation has been performed to demonstrate that these are all
local minima. These all approximate the rotor when using the CaM frame order rotor model synthetic
data.

Fix for the frame_order.permute_axes user function.

One of the 6 permutations had the x and y axes switched (the x <= z <= y condition, permutation A).

Added redirects for all renamed user functions for the HTML version of the manual.

Set up a new redirect for the frq.set to spectrometer.frequency user function name change.

This is for the HTML manual.

Renamed the pseudo-ellipse permutation directory to perm_pseudo_ellipse_x_le_y_le_z.

This is for the CaM frame order rotor model synthetic data.

Updated the frame order pseudo-ellipse motion permutation test data.

This is for the CaM frame order rotor model synthetic data. The correct axis and cone angle
permutations of the frame_order.permute_axes user function are now being used and optimised.

Redesign of the axis permutation algorithm of the frame_order.permute_axes user function.

Instead of tracking the fact that cone_theta_x is a rotation around the y-axis and cone_theta_y is
about the x-axis, now two permutation arrays are created - one for the three angles and one for the
axes. The permutation array values have also been completely changed as previously the incorrect
inverse permutation was coded into the algorithm.

Bug fix for the new frame_order.permute_axes user function.

The cone and torsion angles were not being correctly permuted. Now the direct permutation array is
being used. And the fact that cone_theta_x is a rotation along the y-axis and cone_theta_y along
the x-axis is taken into account.

Created some test data files for visualising the frame order axis permutation.

This uses the CaM frame order synthetic data for the rotor model to visualise the pseudo-ellipse
frame order model axis permutations. The initial conversion sets the pseudo-ellipse torsion angle
cone_sigma_max to the rotor opening half-angle, and the pseudo-elliptic cone opening to close to
zero. Then the axis permutations are performed. All three solutions are optimised. PDB
representations before and after optimisation are included to illustrate any problems.