r9174 - /branches/frame_order/maths_fns/frame_order_models.py -- July 02, 2009 - 03:01

Author: bugman
Date: Thu Jul  2 03:01:41 2009
New Revision: 9174

URL: http://svn.gna.org/viewcvs/relax?rev=9174&view=rev
Log:
Partly reverted r9167 - the previous reversion.

The command used was:
svn merge -r9167:9166 maths_fns/frame_order_models.py


Modified:
    branches/frame_order/maths_fns/frame_order_models.py

Modified: branches/frame_order/maths_fns/frame_order_models.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order/maths_fns/frame_order_models.py?rev=9174&r1=9173&r2=9174&view=diff
==============================================================================
--- branches/frame_order/maths_fns/frame_order_models.py (original)
+++ branches/frame_order/maths_fns/frame_order_models.py Thu Jul  2 03:01:41 
2009
@@ -116,6 +116,10 @@
         self.red_errors = red_errors
         self.red_tensors_bc = zeros(self.num_tensors*5, float64)
 
+        # The cone axis storage and molecular frame z-axis.
+        self.cone_axis = zeros(3, float64)
+        self.z_axis = array([0, 0, 1], float64)
+
         # The rotation to the Frame Order eigenframe.
         self.rot = zeros((3, 3), float64)
         self.tensor_3D = zeros((3, 3), float64)
@@ -142,6 +146,10 @@
         # The errors.
         self.errors = ones((9, 9), float64)
 
+        # The cone axis storage and molecular frame z-axis.
+        self.cone_axis = zeros(3, float64)
+        self.z_axis = array([0, 0, 1], float64)
+
         # The rotation.
         self.rot = zeros((3, 3), float64)
 
@@ -155,12 +163,11 @@
     def func_iso_cone(self, params):
         """Target function for isotropic cone model optimisation using the 
alignment tensors.
 
-        This function optimises against alignment tensors.  The Frame Order 
eigenframe via the
-        alpha, beta, and gamma Euler angles, and the cone angle theta are 
the 4 parameters optimised
-        in this model.
-
-        @param params:  The vector of parameter values {alpha, beta, gamma, 
theta} where the first
-                        three are the Euler angles for the Frame Order 
eigenframe and theta is the
+        This function optimises against alignment tensors.  The cone axis 
spherical angles theta and
+        phi and the cone angle theta are the 3 parameters optimised in this 
model.
+
+        @param params:  The vector of parameter values {theta, phi, 
theta_cone} where the first two
+                        are the polar and azimuthal angles of the cone axis 
theta_cone is the
                         isotropic cone angle.
         @type params:   list of float
         @return:        The chi-squared or SSE value.
@@ -171,7 +178,7 @@
         alpha, beta, gamma, theta, phi, theta_cone = params
 
         # Generate the 2nd degree Frame Order super matrix.
-        self.frame_order_2nd = 
compile_2nd_matrix_iso_cone(self.frame_order_2nd, self.rot, alpha, beta, 
gamma, theta)
+        self.frame_order_2nd = 
compile_2nd_matrix_iso_cone(self.frame_order_2nd, self.rot, self.z_axis, 
self.cone_axis, theta, phi, theta_cone)
 
         # Reduced alignment tensor rotation into the eigenframe.
         R_euler_zyz(self.rot, alpha, beta, gamma)
@@ -197,11 +204,11 @@
         """Target function for isotropic cone model optimisation using the 
Frame Order matrix.
 
         This function optimises by directly matching the elements of the 2nd 
degree Frame Order
-        super matrix.  The Frame Order eigenframe via the alpha, beta, and 
gamma Euler angles, and
-        the cone angle theta are the 4 parameters optimised in this model.
-
-        @param params:  The vector of parameter values {alpha, beta, gamma, 
theta} where the first
-                        three are the Euler angles for the Frame Order 
eigenframe and theta is the
+        super matrix.  The cone axis spherical angles theta and phi and the 
cone angle theta are the
+        3 parameters optimised in this model.
+
+        @param params:  The vector of parameter values {theta, phi, 
theta_cone} where the first two
+                        are the polar and azimuthal angles of the cone axis 
theta_cone is the
                         isotropic cone angle.
         @type params:   list of float
         @return:        The chi-squared or SSE value.
@@ -209,10 +216,10 @@
         """
 
         # Break up the parameters.
-        alpha, beta, gamma, theta = params
+        theta, phi, theta_cone = params
 
         # Generate the 2nd degree Frame Order super matrix.
-        self.frame_order_2nd = 
compile_2nd_matrix_iso_cone(self.frame_order_2nd, self.rot, alpha, beta, 
gamma, theta)
+        self.frame_order_2nd = 
compile_2nd_matrix_iso_cone(self.frame_order_2nd, self.rot, self.z_axis, 
self.cone_axis, theta, phi, theta_cone)
 
         # Make the Frame Order matrix contiguous.
         self.frame_order_2nd = self.frame_order_2nd.copy()