relax SVN archive

Bug fix for the frame_order.simulate user function.

The incorrect model number was being specified and hence the simulation was not starting from the
optimised average domain position but rather the arbitrary position of the original structure.

Speedup and fix for systemtest Relax_disp.test_dx_map_clustered_create_par_file.

The following test was taken out, since this a particular interesting case.
There exist a double minimum, where relax has not found the global minimum.
This is due to not grid searching for R2A, but using the minimum value.

Fix for systemtest Relax_disp.test_cpmg_synthetic_dx_map_points.

Another import line was written to the matplotlib script.

Eliminated the lib.frame_order.iso_cone.populate_*() functions.

The populate_1st_eigenframe_iso_cone() function was unused and incorrect, so it was deleted. The
contents of the populate_2nd_eigenframe_iso_cone() function have been shifted
compile_2nd_matrix_iso_cone() as a separate function is unnecessary. This now matches all the other
lib.frame_order modules.

Updated the frame order matrix element graphs for the free rotor isotropic cone fixes.

The cone S1 parameter has been converted back to the original cone theta opening half-angle,
allowing the 2nd degree frame order matrix elements to be properly calculated for all motions.

Redesign of the free rotor isotropic cone frame order model - the order parameter has been replaced.

From the frame order matrix element graphs in test_suite/shared_data/frame_order/sim_vs_pred_matrix,
specifically Sijkl_iso_cone_free_rotor_in_frame_theta_x_calc.agr,
Sijkl_iso_cone_free_rotor_axis2_1_3_theta_x_calc.agr, and
Sijkl_iso_cone_free_rotor_out_of_frame_theta_x_calc.agr, it is clear that the symmetry of the order
parameter after 120 degrees causes the 2nd degree frame order matrix to be incorrectly estimated.
Therefore the S1 order parameter has been replaced with the original cone opening angle cone_theta.

All parts of relax have been updated for this large conversion.

Merged revisions 26395 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26395 | bugman | 2014-10-28 19:47:10 +0100 (Tue, 28 Oct 2014) | 3 lines

Small indexing fixes for the dispersion chapter of the relax manual.
........

Clean up of the frame order matrix element simulation script.

The 1st pseudo-ellipse torsion angle value in the frame order matrix graphs is now 0.0.

Only the cone opening angles set to 0.0 cause a failure in the pseudo-ellipse models, so the torsion
angle is now allowed to start at exactly zero.

The 1st angle for the calculated frame order matrix graphs is 0 for all non pseudo-ellipse models.

This is for the frame_order_solution.py script. Only the pseudo-ellipse models where numerical
integration is required fail for the angle of 0.0. Therefore the changing of the first angle from
0.0 to 0.01 only occurs for the pseudo-ellipse models. All graphs have been updated.