r22515 - /branches/double_rotor/test_suite/system_tests/scripts/frame_order/cam/base_script.py -- March 21, 2014 - 09:39

Author: bugman
Date: Fri Mar 21 09:39:33 2014
New Revision: 22515

URL: http://svn.gna.org/viewcvs/relax?rev=22515&view=rev
Log:
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.


Modified:
    
branches/double_rotor/test_suite/system_tests/scripts/frame_order/cam/base_script.py

Modified: 
branches/double_rotor/test_suite/system_tests/scripts/frame_order/cam/base_script.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/double_rotor/test_suite/system_tests/scripts/frame_order/cam/base_script.py?rev=22515&r1=22514&r2=22515&view=diff
==============================================================================
--- 
branches/double_rotor/test_suite/system_tests/scripts/frame_order/cam/base_script.py
        (original)
+++ 
branches/double_rotor/test_suite/system_tests/scripts/frame_order/cam/base_script.py
        Fri Mar 21 09:39:33 2014
@@ -23,11 +23,13 @@
 """Base script for the optimisation of the rigid frame order test models."""
 
 # Python module imports.
-from numpy import array, float32, float64, transpose, zeros
+from numpy import arccos, array, cross, dot, float32, float64, transpose, 
zeros
+from numpy.linalg import norm
 from os import F_OK, access, sep
 
 # relax module imports.
 from data_store import Relax_data_store; ds = Relax_data_store()
+from lib.geometry.coord_transform import spherical_to_cartesian
 from lib.geometry.rotations import euler_to_R_zyz, reverse_euler_zyz
 from status import Status; status = Status()
 
@@ -71,9 +73,16 @@
     PIVOT = array([ 37.254, 0.5, 16.7465], float32)
     PIVOT2 = None
 
+    # The CoM - for use in the rotor models.
+    COM = array([44.737253525507697, -1.1684805963699558, 
14.072436716990133], float32)
+
 
     def __init__(self, exec_fn):
         """Execute the frame order analysis."""
+
+        # Parameter conversions.
+        if self.AXIS_THETA != None and self.AXIS_ALPHA == None:
+            self.AXIS_ALPHA = self.convert_rotor(theta=self.AXIS_THETA, 
phi=self.AXIS_PHI, pivot=self.PIVOT, com=self.COM)
 
         # Alias the user function executor method.
         self._execute_uf = exec_fn
@@ -103,6 +112,41 @@
 
         # Save the state.
         self._execute_uf(uf_name='state.save', state='devnull', force=True)
+
+
+    def convert_rotor(self, theta=None, phi=None, pivot=None, com=None):
+        """Convert the rotor axis spherical angles to the axis alpha 
notation.
+
+        @keyword theta: The polar spherical angle.
+        @type theta:    float
+        @keyword phi:   The azimuthal spherical angle.
+        @type phi:      float
+        @keyword pivot: The pivot point on the rotation axis.
+        @type pivot:    numpy rank-1 3D array
+        @keyword com:   The pivot point on the rotation axis.
+        @type com:      numpy rank-1 3D array
+        @return:        The axis alpha angle for the system.
+        @rtype:         float
+        """
+
+        # The CoM-pivot unit vector.
+        com_piv = pivot - com
+        com_piv = com_piv / norm(com_piv)
+
+        # The vector perpendicular to the CoM-pivot vector.
+        z_axis = array([0, 0, 1], float64)
+        perp_vect = cross(com_piv, z_axis)
+        perp_vect = perp_vect / norm(perp_vect)
+
+        # The axis.
+        axis = zeros(3, float64)
+        spherical_to_cartesian([1.0, theta, phi], axis)
+
+        # The alpha angle (the angle between the perpendicular vector and 
the axis).
+        alpha = arccos(dot(perp_vect, axis))
+
+        # Return the axis alpha angle.
+        return alpha
 
 
     def optimisation(self):