relax SVN archive

Changes for the convert_rotor() method of the CaM frame order system test base script.

The method now sets the alpha angle rather than returning it. The method now also resets the pivot
point to the point on the rotation axis closest to the CoM.

Fixes for the rotor axis alpha angle conversion in the CaM frame order system test base script.

The pivot point is not the point on the rotor axis closest to the reference point (the CoM).
Therefore the closest point is now calculated from the pivot point on the axis and the axis vector.
This closest point is needed for defining the new minimal parameter set for the rotor models.

The CaM frame order system test base script is now using lib.geometry.vectors.vector_angle().

This is for correctly calculating the alpha axis angle for the rotor models.

Merged revisions 22518-22520 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r22518 | bugman | 2014-03-21 15:22:38 +0100 (Fri, 21 Mar 2014) | 6 lines

Created the new vector_angle() library function.

This is located in the lib.geometry.vectors module. The function will calculate the angle between
two vectors with sign or direction using the atan2() function.
........
r22519 | bugman | 2014-03-21 17:26:06 +0100 (Fri, 21 Mar 2014) | 3 lines

Addition of a number of unit tests for the new lib.geometry.vectors.vector_angle() function.
........
r22520 | bugman | 2014-03-21 17:29:24 +0100 (Fri, 21 Mar 2014) | 7 lines

Changes to the lib.geometry.vectors.vector_angle() function.

This now expects the normal of the plane in which the angle is defined. The original logic was not
functional, therefore the angle is forced to be negative if the cross product between the two
vectors points in the opposite direction as the normal.
........

Changes to the lib.geometry.vectors.vector_angle() function.

This now expects the normal of the plane in which the angle is defined. The original logic was not
functional, therefore the angle is forced to be negative if the cross product between the two
vectors points in the opposite direction as the normal.

Addition of a number of unit tests for the new lib.geometry.vectors.vector_angle() function.

Created the new vector_angle() library function.

This is located in the lib.geometry.vectors module. The function will calculate the angle between
two vectors with sign or direction using the atan2() function.

Merged revisions 22516 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r22516 | bugman | 2014-03-21 11:09:18 +0100 (Fri, 21 Mar 2014) | 7 lines

Bug fix for all of the R1rho relaxation dispersion models.

The atan2() function is now being used rather than atan() for determining the rotating frame tilt
angle. This is to allow the angle to be in the correct quandrant - i.e. to have a sign or
direction.
........

Bug fix for all of the R1rho relaxation dispersion models.

The atan2() function is now being used rather than atan() for determining the rotating frame tilt
angle. This is to allow the angle to be in the correct quandrant - i.e. to have a sign or
direction.

The CaM frame order system tests for the rotor models are converted to the new axis_alpha parameter.

The axis_theta and axis_phi spherical coordinates are converted to the new reduced parameter set
defined by a random point in space (the CoM of all atoms), the pivot point, and a single angle
alpha.