r11490 - in /1.3/maths_fns: frame_order.py frame_order_matrix_ops.py -- August 12, 2010 - 13:35

Author: bugman
Date: Thu Aug 12 13:35:48 2010
New Revision: 11490

URL: http://svn.gna.org/viewcvs/relax?rev=11490&view=rev
Log:
The rotor frame order model is now functional.


Modified:
    1.3/maths_fns/frame_order.py
    1.3/maths_fns/frame_order_matrix_ops.py

Modified: 1.3/maths_fns/frame_order.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/maths_fns/frame_order.py?rev=11490&r1=11489&r2=11490&view=diff
==============================================================================
--- 1.3/maths_fns/frame_order.py (original)
+++ 1.3/maths_fns/frame_order.py Thu Aug 12 13:35:48 2010
@@ -31,7 +31,7 @@
 from generic_fns.frame_order import print_frame_order_2nd_degree
 from maths_fns.alignment_tensor import to_5D, to_tensor
 from maths_fns.chi2 import chi2
-from maths_fns.frame_order_matrix_ops import compile_2nd_matrix_free_rotor, 
compile_2nd_matrix_iso_cone, 
compile_2nd_matrix_iso_cone_free_rotor,compile_2nd_matrix_iso_cone_torsionless,
 compile_2nd_matrix_pseudo_ellipse, 
compile_2nd_matrix_pseudo_ellipse_free_rotor, 
compile_2nd_matrix_pseudo_ellipse_torsionless, reduce_alignment_tensor
+from maths_fns.frame_order_matrix_ops import compile_2nd_matrix_free_rotor, 
compile_2nd_matrix_iso_cone, 
compile_2nd_matrix_iso_cone_free_rotor,compile_2nd_matrix_iso_cone_torsionless,
 compile_2nd_matrix_pseudo_ellipse, 
compile_2nd_matrix_pseudo_ellipse_free_rotor, 
compile_2nd_matrix_pseudo_ellipse_torsionless, compile_2nd_matrix_rotor, 
reduce_alignment_tensor
 from maths_fns.rotation_matrix import euler_to_R_zyz as euler_to_R
 from relax_errors import RelaxError
 
@@ -403,10 +403,10 @@
         """
 
         # Unpack the parameters.
-        ave_pos_alpha, ave_pos_beta, ave_pos_gamma, axis_theta, axis_phi, 
sigma_max = params
-
-        # Generate the 2nd degree Frame Order super matrix.
-        frame_order_2nd = compile_2nd_matrix_rotor(self.frame_order_2nd, 
self.rot, self.z_axis, self.cone_axis, axis_theta, axis_phi, sigma_max)
+        ave_pos_alpha, ave_pos_beta, ave_pos_gamma, eigen_alpha, eigen_beta, 
eigen_gamma, sigma_max = params
+
+        # Generate the 2nd degree Frame Order super matrix.
+        frame_order_2nd = compile_2nd_matrix_rotor(self.frame_order_2nd, 
self.rot, eigen_alpha, eigen_beta, eigen_gamma, sigma_max)
 
         # Reduce and rotate the tensors.
         self.reduce_and_rot(ave_pos_alpha, ave_pos_beta, ave_pos_gamma, 
frame_order_2nd)

Modified: 1.3/maths_fns/frame_order_matrix_ops.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/maths_fns/frame_order_matrix_ops.py?rev=11490&r1=11489&r2=11490&view=diff
==============================================================================
--- 1.3/maths_fns/frame_order_matrix_ops.py (original)
+++ 1.3/maths_fns/frame_order_matrix_ops.py Thu Aug 12 13:35:48 2010
@@ -402,7 +402,7 @@
     return rotate_daeg(matrix, R)
 
 
-def compile_2nd_matrix_rotor(matrix, R, z_axis, cone_axis, theta_axis, 
phi_axis, smax):
+def compile_2nd_matrix_rotor(matrix, R, eigen_alpha, eigen_beta, 
eigen_gamma, smax):
     """Generate the rotated 2nd degree Frame Order matrix for the rotor 
model.
 
     The cone axis is assumed to be parallel to the z-axis in the eigenframe.
@@ -412,14 +412,12 @@
     @type matrix:       numpy 9D, rank-2 array
     @param R:           The rotation matrix to be populated.
     @type R:            numpy 3D, rank-2 array
-    @param z_axis:      The molecular frame z-axis from which the cone axis 
is rotated from.
-    @type z_axis:       numpy 3D, rank-1 array
-    @param cone_axis:   The storage structure for the cone axis.
-    @type cone_axis:    numpy 3D, rank-1 array
-    @param theta_axis:  The cone axis polar angle.
-    @type theta_axis:   float
-    @param phi_axis:    The cone axis azimuthal angle.
-    @type phi_axis:     float
+    @param eigen_alpha: The eigenframe rotation alpha Euler angle.
+    @type eigen_alpha:  float
+    @param eigen_beta:  The eigenframe rotation beta Euler angle.
+    @type eigen_beta:   float
+    @param eigen_gamma: The eigenframe rotation gamma Euler angle.
+    @type eigen_gamma:  float
     @param smax:        The maximum torsion angle.
     @type smax:         float
     """
@@ -450,11 +448,8 @@
     # Off diagonal set 2.
     matrix[1, 3] = matrix[3, 1] = -matrix[0, 4]
 
-    # Generate the cone axis from the spherical angles.
-    spherical_to_cartesian([1.0, theta_axis, phi_axis], cone_axis)
-
     # Average position rotation.
-    two_vect_to_R(z_axis, cone_axis, R)
+    euler_to_R_zyz(eigen_alpha, eigen_beta, eigen_gamma, R)
 
     # Rotate and return the frame order matrix.
     return rotate_daeg(matrix, R)