r22627 - in /trunk: ./ test_suite/shared_data/frame_order/cam/ test_suite/shared_data/frame_order/cam/double_rotor/ -- April 03, 2014 - 19:29

Author: bugman
Date: Thu Apr  3 19:29:44 2014
New Revision: 22627

URL: http://svn.gna.org/viewcvs/relax?rev=22627&view=rev
Log:
Merged revisions 22022-22023 via svnmerge from 
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/double_rotor

........
  r22022 | bugman | 2014-01-16 18:39:42 +0100 (Thu, 16 Jan 2014) | 3 lines
  
  Created a directory for holding the CaM double rotor frame order synthetic 
data.
........
  r22023 | bugman | 2014-01-17 09:40:42 +0100 (Fri, 17 Jan 2014) | 3 lines
  
  Capitalised the pivot and CoM variables in the base frame order 
distribution generation script.
........

Added:
    trunk/test_suite/shared_data/frame_order/cam/double_rotor/
      - copied from r22023, 
branches/double_rotor/test_suite/shared_data/frame_order/cam/double_rotor/
Modified:
    trunk/   (props changed)
    trunk/test_suite/shared_data/frame_order/cam/generate_base.py

Propchange: trunk/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Thu Apr  3 19:29:44 2014
@@ -1 +1 @@
-/branches/double_rotor:1-21950
+/branches/double_rotor:1-21950,22022-22023

Modified: trunk/test_suite/shared_data/frame_order/cam/generate_base.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/generate_base.py?rev=22627&r1=22626&r2=22627&view=diff
==============================================================================
--- trunk/test_suite/shared_data/frame_order/cam/generate_base.py       
(original)
+++ trunk/test_suite/shared_data/frame_order/cam/generate_base.py       Thu 
Apr  3 19:29:44 2014
@@ -45,8 +45,8 @@
 
 class Main:
     # The pivot and CoM for the CaM system.
-    pivot = array([ 37.254, 0.5, 16.7465])
-    com = array([ 26.83678091, -12.37906417,  28.34154128])
+    PIVOT = array([ 37.254, 0.5, 16.7465])
+    COM = array([ 26.83678091, -12.37906417,  28.34154128])
 
     def run(self, save_path=None):
         """Generate the distribution and alignment data.
@@ -188,7 +188,7 @@
             # Rotate the atomic position.
             for spin in spin_loop():
                 if hasattr(spin, 'pos'):
-                    spin.pos[i] = dot(self.R, (spin.orig_pos[0] - 
self.pivot)) + self.pivot
+                    spin.pos[i] = dot(self.R, (spin.orig_pos[0] - 
self.PIVOT)) + self.PIVOT
 
             # Rotate the NH vector.
             for interatom in interatomic_loop():
@@ -271,12 +271,12 @@
         self.interpreter.pipe.create('axes', 'N-state')
 
         # The end points of the vectors.
-        end_pt_x = self.axes[:, 0] * norm(self.com - self.pivot) + self.pivot
-        end_pt_y = self.axes[:, 1] * norm(self.com - self.pivot) + self.pivot
-        end_pt_z = self.axes[:, 2] * norm(self.com - self.pivot) + self.pivot
+        end_pt_x = self.axes[:, 0] * norm(self.COM - self.PIVOT) + self.PIVOT
+        end_pt_y = self.axes[:, 1] * norm(self.COM - self.PIVOT) + self.PIVOT
+        end_pt_z = self.axes[:, 2] * norm(self.COM - self.PIVOT) + self.PIVOT
 
         # Add atoms for the system.
-        self.interpreter.structure.add_atom(atom_name='C', res_name='AXE', 
res_num=1, pos=self.pivot, element='C')
+        self.interpreter.structure.add_atom(atom_name='C', res_name='AXE', 
res_num=1, pos=self.PIVOT, element='C')
         self.interpreter.structure.add_atom(atom_name='N', res_name='AXE', 
res_num=1, pos=end_pt_x, element='N')
         self.interpreter.structure.add_atom(atom_name='N', res_name='AXE', 
res_num=1, pos=end_pt_y, element='N')
         self.interpreter.structure.add_atom(atom_name='N', res_name='AXE', 
res_num=1, pos=end_pt_z, element='N')
@@ -297,10 +297,10 @@
         self.interpreter.pipe.create('axes', 'N-state')
 
         # The end points of the vectors.
-        end_pt = self.axes[:, 2] * norm(self.com - self.pivot) + self.pivot
+        end_pt = self.axes[:, 2] * norm(self.COM - self.PIVOT) + self.PIVOT
 
         # Add atoms for the system.
-        self.interpreter.structure.add_atom(atom_name='C', res_name='AXE', 
res_num=1, pos=self.pivot, element='C')
+        self.interpreter.structure.add_atom(atom_name='C', res_name='AXE', 
res_num=1, pos=self.PIVOT, element='C')
         self.interpreter.structure.add_atom(atom_name='N', res_name='AXE', 
res_num=1, pos=end_pt, element='N')
 
         # Connect the atoms to form the vectors.
@@ -314,7 +314,7 @@
         """An alternative axis system for the CaM system."""
 
         # The z-axis for the rotations (the pivot point to CoM axis).
-        axis_z = self.com - self.pivot
+        axis_z = self.COM - self.PIVOT
         axis_z = axis_z / norm(axis_z)
 
         # The y-axis (to check the torsion angle).
@@ -352,7 +352,7 @@
         """A standard axis system for the CaM system with the z-axis along 
the pivot-com axis."""
 
         # The z-axis for the rotations (the pivot point to CoM axis).
-        axis_z = self.com - self.pivot
+        axis_z = self.COM - self.PIVOT
         axis_z = axis_z / norm(axis_z)
 
         # The y-axis (to check the torsion angle).