r9078 - /branches/frame_order/maths_fns/frame_order_models.py -- June 18, 2009 - 10:42

Author: bugman
Date: Thu Jun 18 10:42:31 2009
New Revision: 9078

URL: http://svn.gna.org/viewcvs/relax?rev=9078&view=rev
Log:
Added the Frame Order target function class.

It currently contains only one target function for an isotropic cone model 
directly optimised to the
Frame Order matrix elements.


Added:
    branches/frame_order/maths_fns/frame_order_models.py

Added: 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=9078&view=auto
==============================================================================
--- branches/frame_order/maths_fns/frame_order_models.py (added)
+++ branches/frame_order/maths_fns/frame_order_models.py Thu Jun 18 10:42:31 
2009
@@ -1,0 +1,109 @@
+###############################################################################
+#                                                                            
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+# Copyright (C) 2009 Edward d'Auvergne                                       
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+#                                                                            
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+# This file is part of the program relax.                                    
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+#                                                                            
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+# relax is free software; you can redistribute it and/or modify              
 #
+# it under the terms of the GNU General Public License as published by       
 #
+# the Free Software Foundation; either version 2 of the License, or          
 #
+# (at your option) any later version.                                        
 #
+#                                                                            
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+# relax is distributed in the hope that it will be useful,                   
 #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of             
 #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the              
 #
+# GNU General Public License for more details.                               
 #
+#                                                                            
 #
+# You should have received a copy of the GNU General Public License          
 #
+# along with relax; if not, write to the Free Software                       
 #
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA  
 #
+#                                                                            
 #
+###############################################################################
+
+# Module docstring.
+"""Module containing the target functions of the Frame Order theories."""
+
+# Python module imports.
+from numpy import dot, float64, ones, transpose, zeros
+
+# relax module imports.
+from maths_fns.chi2 import chi2
+from maths_fns.frame_order_matrix_ops import populate_2nd_eigenframe_iso_cone
+from maths_fns.kronecker_product import kron_prod, transpose_14
+from maths_fns.rotation_matrix import R_euler_zyz
+
+
+class Frame_order:
+    """Class containing the target function of the optimisation of Frame 
Order matrix components."""
+
+    def __init__(self, frame_order_matrix=None):
+        """Set up the target functions for the Frame Order theories."""
+
+        # Optimisation to the 2nd degree Frame Order matrix components 
directly.
+        if frame_order_matrix:
+            # Store the real matrix components.
+            self.data = data
+
+            # The errors.
+            self.errors = ones((9, 9), float64)
+
+            # The rotation.
+            self.rot = zeros((3, 3), float64)
+
+            # Initialise the Frame Order matrices.
+            self.frame_order_1st = zeros((3, 3), float64)
+            self.frame_order_2nd = zeros((9, 9), float64)
+
+
+    def func_iso_cone_elements(self, params):
+        """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.
+        @type params:   list of float
+        @return:        The chi-squared or SSE value.
+        @rtype:         float
+        """
+
+        # Break up the parameters.
+        alpha, beta, gamma, theta = params
+
+        # Populate the Frame Order matrix in the eigenframe.
+        populate_2nd_eigenframe_iso_cone(self.frame_order_2nd, theta)
+
+        # Generate the rotation matrix.
+        R_euler_zyz(self.rot, alpha, beta, gamma)
+
+        # The outer product of R.
+        R_kron = kron_prod(self.rot, self.rot)
+
+        # Perform the T14 transpose to obtain the Kronecker product matrix!
+        self.frame_order_2nd = transpose_14(self.frame_order_2nd)
+
+        # Rotate.
+        self.frame_order_2nd = dot(R_kron, dot(self.frame_order_2nd, 
transpose(R_kron)))
+
+        # Perform T14 again to return back.
+        self.frame_order_2nd = transpose_14(self.frame_order_2nd)
+
+        # Make the Frame Order contiguous.
+        self.frame_order_2nd = self.frame_order_2nd.copy()
+
+        # Reshape the numpy arrays for use in the chi2() function.
+        self.data.shape = (81,)
+        self.frame_order_2nd.shape = (81,)
+        self.errors.shape = (81,)
+
+        # Get the chi-squared value.
+        val = chi2(self.data, self.frame_order_2nd, self.errors)
+
+        # Reshape the arrays back to normal.
+        self.data.shape = (9, 9)
+        self.frame_order_2nd.shape = (9, 9)
+        self.errors.shape = (9, 9)
+
+        # Return the chi2 value.
+        return val