Author: bugman
Date: Wed Aug 11 23:56:45 2010
New Revision: 11480
URL: http://svn.gna.org/viewcvs/relax?rev=11480&view=rev
Log:
Created the free rotor frame order model.
Modified:
1.3/maths_fns/frame_order.py
1.3/maths_fns/frame_order_matrix_ops.py
Modified: 1.3/maths_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/maths_fns/frame_order.py?rev=11480&r1=11479&r2=11480&view=diff
==============================================================================
--- 1.3/maths_fns/frame_order.py (original)
+++ 1.3/maths_fns/frame_order.py Wed Aug 11 23:56:45 2010
@@ -31,7 +31,7 @@
from generic_fns.frame_order import print_frame_order_2nd_degree
from maths_fns.alignment_tensor import to_5D, to_tensor
from maths_fns.chi2 import chi2
-from maths_fns.frame_order_matrix_ops import compile_2nd_matrix_iso_cone,
compile_2nd_matrix_iso_cone_free_rotor,compile_2nd_matrix_iso_cone_torsionless,
compile_2nd_matrix_pseudo_ellipse,
compile_2nd_matrix_pseudo_ellipse_free_rotor,
compile_2nd_matrix_pseudo_ellipse_torsionless, reduce_alignment_tensor
+from maths_fns.frame_order_matrix_ops import compile_2nd_matrix_free_rotor,
compile_2nd_matrix_iso_cone,
compile_2nd_matrix_iso_cone_free_rotor,compile_2nd_matrix_iso_cone_torsionless,
compile_2nd_matrix_pseudo_ellipse,
compile_2nd_matrix_pseudo_ellipse_free_rotor,
compile_2nd_matrix_pseudo_ellipse_torsionless, reduce_alignment_tensor
from maths_fns.rotation_matrix import euler_to_R_zyz as euler_to_R
from relax_errors import RelaxError
@@ -169,6 +169,30 @@
self.func = self.func_iso_cone_elements
+ def func_free_rotor(self, params):
+ """Target function for free rotor model optimisation.
+
+ This function optimises against alignment tensors. The Euler angles
for the tensor rotation are the first 3 parameters optimised in this model,
followed by the polar and azimuthal angles of the cone axis.
+
+ @param params: The vector of parameter values. These are the
tensor rotation angles {alpha, beta, gamma, theta, phi}.
+ @type params: list of float
+ @return: The chi-squared or SSE value.
+ @rtype: float
+ """
+
+ # Unpack the parameters.
+ ave_pos_beta, ave_pos_gamma, axis_theta, axis_phi = params
+
+ # Generate the 2nd degree Frame Order super matrix.
+ frame_order_2nd =
compile_2nd_matrix_free_rotor(self.frame_order_2nd, self.rot, self.z_axis,
self.cone_axis, axis_theta, axis_phi)
+
+ # Reduce and rotate the tensors.
+ self.reduce_and_rot(0.0, ave_pos_beta, ave_pos_gamma,
frame_order_2nd)
+
+ # Return the chi-squared value.
+ return chi2(self.red_tensors, self.red_tensors_bc, self.red_errors)
+
+
def func_iso_cone_elements(self, params):
"""Target function for isotropic cone model optimisation using the
Frame Order matrix.
Modified: 1.3/maths_fns/frame_order_matrix_ops.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/maths_fns/frame_order_matrix_ops.py?rev=11480&r1=11479&r2=11480&view=diff
==============================================================================
--- 1.3/maths_fns/frame_order_matrix_ops.py (original)
+++ 1.3/maths_fns/frame_order_matrix_ops.py Wed Aug 11 23:56:45 2010
@@ -58,6 +58,54 @@
matrix[0, 0] = fact * quad(part_int_daeg1_pseudo_ellipse_xx, -pi, pi,
args=(theta_x, theta_y, sigma_max), full_output=1)[0]
matrix[1, 1] = fact * quad(part_int_daeg1_pseudo_ellipse_yy, -pi, pi,
args=(theta_x, theta_y, sigma_max), full_output=1)[0]
matrix[2, 2] = fact * quad(part_int_daeg1_pseudo_ellipse_zz, -pi, pi,
args=(theta_x, theta_y, sigma_max), full_output=1)[0]
+
+
+def compile_2nd_matrix_free_rotor(matrix, R, z_axis, axis, theta_axis,
phi_axis):
+ """Generate the rotated 2nd degree Frame Order matrix for the free rotor
model.
+
+ The rotor axis is assumed to be parallel to the z-axis in the eigenframe.
+
+
+ @param matrix: The Frame Order matrix, 2nd degree to be populated.
+ @type matrix: numpy 9D, rank-2 array
+ @param R: The rotation matrix to be populated.
+ @type R: numpy 3D, rank-2 array
+ @param z_axis: The molecular frame z-axis from which the rotor axis
is rotated from.
+ @type z_axis: numpy 3D, rank-1 array
+ @param axis: The storage structure for the axis.
+ @type axis: numpy 3D, rank-1 array
+ @param theta_axis: The axis polar angle.
+ @type theta_axis: float
+ @param phi_axis: The axis azimuthal angle.
+ @type phi_axis: float
+ """
+
+ # Zeros.
+ for i in range(9):
+ for j in range(9):
+ matrix[i, j] = 0.0
+
+ # Diagonal.
+ matrix[0, 0] = 0.5
+ matrix[1, 1] = 0.5
+ matrix[3, 3] = 0.5
+ matrix[4, 4] = 0.5
+ matrix[8, 8] = 1
+
+ # Off diagonal set 1.
+ matrix[0, 4] = matrix[4, 0] = 0.5
+
+ # Off diagonal set 2.
+ matrix[1, 3] = matrix[3, 1] = -0.5
+
+ # Generate the cone axis from the spherical angles.
+ spherical_to_cartesian([1.0, theta_axis, phi_axis], axis)
+
+ # Average position rotation.
+ two_vect_to_R(z_axis, axis, R)
+
+ # Rotate and return the frame order matrix.
+ return rotate_daeg(matrix, R)
def compile_2nd_matrix_iso_cone(matrix, R, eigen_alpha, eigen_beta,
eigen_gamma, cone_theta, sigma_max):
r11480 - in /1.3/maths_fns: frame_order.py frame_order_matrix_ops.py