Author: bugman
Date: Wed Aug 11 18:37:35 2010
New Revision: 11473
URL: http://svn.gna.org/viewcvs/relax?rev=11473&view=rev
Log:
Implemented the torsionless isotropic cone 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=11473&r1=11472&r2=11473&view=diff
==============================================================================
--- 1.3/maths_fns/frame_order.py (original)
+++ 1.3/maths_fns/frame_order.py Wed Aug 11 18:37:35 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_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_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
@@ -256,6 +256,30 @@
return chi2(self.red_tensors, self.red_tensors_bc, self.red_errors)
+ def func_iso_cone_torsionless(self, params):
+ """Target function for torsionless isotropic cone model optimisation.
+
+ This function optimises against alignment tensors.
+
+ @param params: The vector of parameter values {beta, gamma, theta,
phi, cone_theta} where the first 2 are the tensor rotation Euler angles, the
next two are the polar and azimuthal angles of the cone axis, and cone_theta
is cone opening angle.
+ @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, cone_theta =
params
+
+ # Generate the 2nd degree Frame Order super matrix.
+ frame_order_2nd =
compile_2nd_matrix_iso_cone_torsionless(self.frame_order_2nd, self.rot,
self.z_axis, self.cone_axis, axis_theta, axis_phi, cone_theta)
+
+ # 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_pseudo_ellipse(self, params):
"""Target function for pseudo-elliptic cone model optimisation.
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=11473&r1=11472&r2=11473&view=diff
==============================================================================
--- 1.3/maths_fns/frame_order_matrix_ops.py (original)
+++ 1.3/maths_fns/frame_order_matrix_ops.py Wed Aug 11 18:37:35 2010
@@ -121,6 +121,68 @@
# Populate the Frame Order matrix in the eigenframe.
populate_2nd_eigenframe_iso_cone_free_rotor(matrix, s1)
+
+ # Average position rotation.
+ two_vect_to_R(z_axis, cone_axis, R)
+
+ # Rotate and return the frame order matrix.
+ return rotate_daeg(matrix, R)
+
+
+def compile_2nd_matrix_iso_cone_torsionless(matrix, R, z_axis, cone_axis,
theta_axis, phi_axis, cone_theta):
+ """Generate the rotated 2nd degree Frame Order matrix for the
torsionless isotropic cone.
+
+ The cone 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 cone axis
is rotated from.
+ @type z_axis: numpy 3D, rank-1 array
+ @param cone_axis: The storage structure for the cone axis.
+ @type cone_axis: numpy 3D, rank-1 array
+ @param theta_axis: The cone axis polar angle.
+ @type theta_axis: float
+ @param phi_axis: The cone axis azimuthal angle.
+ @type phi_axis: float
+ @param cone_theta: The cone opening angle.
+ @type cone_theta: float
+ """
+
+ # Zeros.
+ for i in range(9):
+ for j in range(9):
+ matrix[i, j] = 0.0
+
+ # Repetitive trig calculations.
+ cos_tmax = cos(cone_theta)
+ cos_tmax2 = cos_tmax**2
+
+ # Diagonal.
+ matrix[0, 0] = (3.0*cos_tmax2 + 6.0*cos_tmax + 15.0) / 24.0
+ matrix[1, 1] = (cos_tmax2 + 10.0*cos_tmax + 13.0) / 24.0
+ matrix[2, 2] = (4.0*cos_tmax2 + 10.0*cos_tmax + 10.0) / 24.0
+ matrix[3, 3] = matrix[1, 1]
+ matrix[4, 4] = matrix[0, 0]
+ matrix[5, 5] = matrix[2, 2]
+ matrix[6, 6] = matrix[2, 2]
+ matrix[7, 7] = matrix[2, 2]
+ matrix[8, 8] = (cos_tmax2 + cos_tmax + 1.0) / 3.0
+
+ # Off diagonal set 1.
+ matrix[0, 4] = matrix[4, 0] = (cos_tmax2 - 2.0*cos_tmax + 1.0) / 24.0
+ matrix[0, 8] = matrix[8, 0] = -(cos_tmax2 + cos_tmax - 2.0) / 6.0
+ matrix[4, 8] = matrix[8, 4] = matrix[0, 8]
+
+ # Off diagonal set 2.
+ matrix[1, 3] = matrix[3, 1] = matrix[0, 4]
+ matrix[2, 6] = matrix[6, 2] = -matrix[0, 8]
+ matrix[5, 7] = matrix[7, 5] = -matrix[0, 8]
+
+ # Generate the cone axis from the spherical angles.
+ spherical_to_cartesian([1.0, theta_axis, phi_axis], cone_axis)
# Average position rotation.
two_vect_to_R(z_axis, cone_axis, R)
r11473 - in /1.3/maths_fns: frame_order.py frame_order_matrix_ops.py