r23683 - in /branches/frame_order_cleanup: specific_analyses/frame_order/ target_functions/ -- June 06, 2014 - 10:26

Author: bugman
Date: Fri Jun  6 10:26:20 2014
New Revision: 23683

URL: http://svn.gna.org/viewcvs/relax?rev=23683&view=rev
Log:
Converted the 'free rotor' frame order model to the new axis_alpha parameter 
system.

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.  The alpha parameter defines the rotor axis angle from the xy-plane.


Modified:
    branches/frame_order_cleanup/specific_analyses/frame_order/optimisation.py
    branches/frame_order_cleanup/specific_analyses/frame_order/parameters.py
    branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
    branches/frame_order_cleanup/target_functions/frame_order.py

Modified: 
branches/frame_order_cleanup/specific_analyses/frame_order/optimisation.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/frame_order/optimisation.py?rev=23683&r1=23682&r2=23683&view=diff
==============================================================================
--- 
branches/frame_order_cleanup/specific_analyses/frame_order/optimisation.py  
(original)
+++ 
branches/frame_order_cleanup/specific_analyses/frame_order/optimisation.py  
Fri Jun  6 10:26:20 2014
@@ -679,7 +679,7 @@
 
     # The centre of mass, for use in the rotor models.
     com = None
-    if cdp.model in ['rotor', 'double rotor']:
+    if cdp.model in ['rotor', 'free rotor', 'double rotor']:
         # The centre of mass of all objects in the data pipe.
         com = pipe_centre_of_mass(verbosity=0)
         com = array(com, float64)

Modified: 
branches/frame_order_cleanup/specific_analyses/frame_order/parameters.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/frame_order/parameters.py?rev=23683&r1=23682&r2=23683&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/frame_order/parameters.py  
  (original)
+++ branches/frame_order_cleanup/specific_analyses/frame_order/parameters.py  
  Fri Jun  6 10:26:20 2014
@@ -238,7 +238,7 @@
         cdp.params.append('eigen_gamma')
 
     # Frame order eigenframe - the isotropic cone axis.
-    if cdp.model in ['iso cone', 'free rotor', 'iso cone, torsionless', 'iso 
cone, free rotor', 'double rotor']:
+    if cdp.model in ['iso cone', 'iso cone, torsionless', 'iso cone, free 
rotor', 'double rotor']:
         cdp.params.append('axis_theta')
         cdp.params.append('axis_phi')
 
@@ -248,7 +248,7 @@
         cdp.params.append('axis_phi_2')
 
     # Frame order eigenframe - the rotor axis alpha angle.
-    if cdp.model in ['rotor']:
+    if cdp.model in ['rotor', 'free rotor']:
         cdp.params.append('axis_alpha')
 
     # Cone parameters - pseudo-elliptic cone parameters.

Modified: branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/frame_order/uf.py?rev=23683&r1=23682&r2=23683&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/frame_order/uf.py    
(original)
+++ branches/frame_order_cleanup/specific_analyses/frame_order/uf.py    Fri 
Jun  6 10:26:20 2014
@@ -176,9 +176,9 @@
             com = pipe_centre_of_mass(verbosity=0)
 
         # Generate the rotor axis.
-        if cdp.model in ['rotor']:
+        if cdp.model in ['rotor', 'free rotor']:
             axis = create_rotor_axis_alpha(alpha=cdp.axis_alpha, 
pivot=pivot, point=com)
-        elif cdp.model in ['free rotor', 'iso cone', 'iso cone, free rotor']:
+        elif cdp.model in ['iso cone', 'iso cone, free rotor']:
             axis = create_rotor_axis_spherical(theta=cdp.axis_theta, 
phi=cdp.axis_phi)
         else:
             axis = create_rotor_axis_euler(alpha=cdp.eigen_alpha, 
beta=cdp.eigen_beta, gamma=cdp.eigen_gamma)

Modified: branches/frame_order_cleanup/target_functions/frame_order.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/target_functions/frame_order.py?rev=23683&r1=23682&r2=23683&view=diff
==============================================================================
--- branches/frame_order_cleanup/target_functions/frame_order.py        
(original)
+++ branches/frame_order_cleanup/target_functions/frame_order.py        Fri 
Jun  6 10:26:20 2014
@@ -131,6 +131,7 @@
         self.paramag_centre = paramag_centre
         self.total_num_params = len(init_params)
         self.num_int_pts = num_int_pts
+        print com
         self.com = com
         self.ave_pos_pivot = ave_pos_pivot
         self._param_pivot = pivot
@@ -467,13 +468,13 @@
         if self.pivot_opt:
             self._param_pivot = params[:3]
             self._translation_vector = params[3:6]
-            ave_pos_beta, ave_pos_gamma, axis_theta, axis_phi = params[6:]
+            ave_pos_beta, ave_pos_gamma, axis_alpha = params[6:]
         else:
             self._translation_vector = params[:3]
-            ave_pos_beta, ave_pos_gamma, axis_theta, axis_phi = params[3:]
-
-        # Generate the cone axis from the spherical angles.
-        spherical_to_cartesian([1.0, axis_theta, axis_phi], self.cone_axis)
+            ave_pos_beta, ave_pos_gamma, axis_alpha = params[3:]
+
+        # Generate the rotor axis.
+        self.cone_axis = create_rotor_axis_alpha(alpha=axis_alpha, 
pivot=array(self._param_pivot, float64), point=self.com)
 
         # Pre-calculate the eigenframe rotation matrix.
         two_vect_to_R(self.z_axis, self.cone_axis, self.R_eigen)