r22525 - /branches/double_rotor/target_functions/frame_order.py -- March 25, 2014 - 10:08

Author: bugman
Date: Tue Mar 25 10:08:00 2014
New Revision: 22525

URL: http://svn.gna.org/viewcvs/relax?rev=22525&view=rev
Log:
Fixes for the rotor axis reconstruction in the func_rotor_qrint() frame order 
target function.

This is for the rotor model.  The axis alpha angle is now correctly converted 
into the rotor axis
using the CoM and pivot point.


Modified:
    branches/double_rotor/target_functions/frame_order.py

Modified: branches/double_rotor/target_functions/frame_order.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/double_rotor/target_functions/frame_order.py?rev=22525&r1=22524&r2=22525&view=diff
==============================================================================
--- branches/double_rotor/target_functions/frame_order.py       (original)
+++ branches/double_rotor/target_functions/frame_order.py       Tue Mar 25 
10:08:00 2014
@@ -47,6 +47,7 @@
 from lib.frame_order.rotor import compile_2nd_matrix_rotor, 
pcs_numeric_int_rotor, pcs_numeric_int_rotor_qrint
 from lib.geometry.coord_transform import spherical_to_cartesian
 from lib.geometry.rotations import axis_angle_to_R, euler_to_R_zyz, 
two_vect_to_R
+from lib.geometry.vectors import vector_angle
 from lib.linear_algebra.kronecker_product import kron_prod
 from lib.order import order_parameters
 from lib.physical_constants import pcs_constant
@@ -1895,12 +1896,16 @@
         else:
             ave_pos_alpha, ave_pos_beta, ave_pos_gamma, axis_alpha, 
sigma_max = params
 
-        # Generate the rotation axis from the CoM, pivot point, and alpha 
angle.
-        r_compiv = array(self._param_pivot, float64) - self.com
-        r_compiv = r_compiv / norm(r_compiv)
-        mu_xy = cross(r_compiv, self.z_axis)
+        # The CoM-pivot unit vector (the pivot is defined as the point on 
the axis closest to the CoM).
+        piv_com = self.com - array(self._param_pivot, float64)
+        piv_com = piv_com / norm(piv_com)
+
+        # The vector perpendicular to the CoM-pivot vector and in the xy 
plane.
+        mu_xy = cross(piv_com, self.z_axis)
         mu_xy = mu_xy / norm(mu_xy)
-        axis_angle_to_R(r_compiv, axis_alpha, self.R)
+
+        # Rotate the vector about the CoM-pivot axis by the angle alpha.
+        axis_angle_to_R(piv_com, axis_alpha, self.R)
         self.cone_axis = dot(self.R, mu_xy)
 
         # Pre-calculate the eigenframe rotation matrix.