relax SVN archive

Fix for the frame order matrix calculation for a pseudo-elliptic cone with angles of zero degrees.

The lib.frame_order.pseudo_ellipse_torsionless.compile_2nd_matrix_pseudo_ellipse_torsionless()
function has been changed to prevent a divide by zero failure. The surface area normalisation
factor now defaults to 0.0.

Modified the rigid_test.py system test script to really be the rigid case.

This is used in all of the Frame_order.test_rigid_data_to_*_model system tests. Previously the
parameters of the dynamics were set to being close to zero, to catch the cases were a few Sobol'
PCS integration points were accepted. But now the case were no Sobol' points can be used is being
tested. This checks a code path currently untested in the test suite, demonstrating many failures.

Added a timeit script and log file for different ways of checking a binary numpy array.

The frame_order.pdb_model user function no longer tries to create a cone object for the double rotor.

Updated the double rotor frame order model to be in a pseudo-functional state.

Bugs in the target function method have been removed, the calc_vectors() target function now accepts
the pivot2 argument (but does nothing with it yet), and the lib.frame_order.double_rotor module has
been updated to match the logic used in all other lib.frame_order modules.

The frame order target function calc_vectors() method arguments have all been converted to keywords.

This is in preparation for handling a second pivot argument for the double rotor model.

Updated all of the CaM frame order system tests for the recent speed up (r23970).

The speed up switched to the use of numpy.tensordot() for shifting each Sobol' rotation into the
eigenframe rather than the previous numpy.dot(). Strangely this affects the precision and hence the
chi-squared value calculated for each system test - both increasing and decreasing it randomly.

Attempt at speeding up the torsionless pseudo-ellipse frame order model.

The check if the Sobol' point is outside of an isotropic cone defined by the largest angle theta_y
is now performed to avoid many unnecessary calls to the tmax_pseudo_ellipse() function.

This however reveals a problem with the test suite data for this model.

Small speed ups for all of the frame order models in the quasi-random numerical PCS integration.

These changes result in an ~10% speed up. Testing via the func_pseudo_ellipse() target function
using the relax profiling flag, the time for one optimisation decreased from 158 to 146 seconds.

The changes consist of pre-calculating all rotations of the rotation matrix into the motional
eigenframe in one mathematical operation rather than one operation per Sobol' point rotation,
unpacking the Sobol' points into the respective angles prior to looping over the points, and taking
the absolute value of the torsion angle and testing if it is out of the bounds rather than checking
both the negative and positive values.

Added the full optimisation results for the torsionless isotropic cone frame order model.

This is for the CaM test data using the new frame_order.py optimisation script.