Author: bugman
Date: Wed Aug 11 23:03:37 2010
New Revision: 11474
URL: http://svn.gna.org/viewcvs/relax?rev=11474&view=rev
Log:
Implemented the rotor frame order matrix model.
This includes the addition of the target function and a unit test.
Modified:
1.3/maths_fns/frame_order.py
1.3/maths_fns/frame_order_matrix_ops.py
1.3/test_suite/unit_tests/_maths_fns/test_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=11474&r1=11473&r2=11474&view=diff
==============================================================================
--- 1.3/maths_fns/frame_order.py (original)
+++ 1.3/maths_fns/frame_order.py Wed Aug 11 23:03:37 2010
@@ -367,6 +367,30 @@
return chi2(self.red_tensors, self.red_tensors_bc, self.red_errors)
+ def func_rotor(self, params):
+ """Target function for 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 and the torsion
angle restriction.
+
+ @param params: The vector of parameter values. These are the
tensor rotation angles {alpha, beta, gamma, theta, phi, sigma_max}.
+ @type params: list of float
+ @return: The chi-squared or SSE value.
+ @rtype: float
+ """
+
+ # Unpack the parameters.
+ ave_pos_alpha, ave_pos_beta, ave_pos_gamma, axis_theta, axis_phi,
sigma_max = params
+
+ # Generate the 2nd degree Frame Order super matrix.
+ frame_order_2nd = compile_2nd_matrix_rotor(self.frame_order_2nd,
self.rot, self.z_axis, self.cone_axis, axis_theta, axis_phi, sigma_max)
+
+ # Reduce and rotate the tensors.
+ self.reduce_and_rot(ave_pos_alpha, 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 reduce_and_rot(self, ave_pos_alpha=None, ave_pos_beta=None,
ave_pos_gamma=None, daeg=None):
"""Reduce and rotate the alignments tensors using the frame order
matrix and Euler angles.
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=11474&r1=11473&r2=11474&view=diff
==============================================================================
--- 1.3/maths_fns/frame_order_matrix_ops.py (original)
+++ 1.3/maths_fns/frame_order_matrix_ops.py Wed Aug 11 23:03:37 2010
@@ -349,6 +349,64 @@
# Average position rotation.
euler_to_R_zyz(eigen_alpha, eigen_beta, eigen_gamma, R)
+
+ # Rotate and return the frame order matrix.
+ return rotate_daeg(matrix, R)
+
+
+def compile_2nd_matrix_rotor(matrix, R, z_axis, cone_axis, theta_axis,
phi_axis, smax):
+ """Generate the rotated 2nd degree Frame Order matrix for the rotor
model.
+
+ 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 smax: The maximum torsion angle.
+ @type smax: float
+ """
+
+ # Zeros.
+ for i in range(9):
+ for j in range(9):
+ matrix[i, j] = 0.0
+
+ # Repetitive trig calculations.
+ sinc_smax = sinc(smax/pi)
+ sinc_2smax = sinc(2.0*smax/pi)
+
+ # Diagonal.
+ matrix[0, 0] = (sinc_2smax + 1.0) / 2.0
+ matrix[1, 1] = matrix[0, 0]
+ matrix[2, 2] = sinc_smax
+ matrix[3, 3] = matrix[0, 0]
+ 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] = 1.0
+
+ # Off diagonal set 1.
+ matrix[0, 4] = matrix[4, 0] = -(sinc_2smax - 1.0) / 2.0
+
+ # Off diagonal set 2.
+ matrix[1, 3] = matrix[3, 1] = -matrix[0, 4]
+
+ # 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)
# Rotate and return the frame order matrix.
return rotate_daeg(matrix, R)
Modified: 1.3/test_suite/unit_tests/_maths_fns/test_frame_order_matrix_ops.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/unit_tests/_maths_fns/test_frame_order_matrix_ops.py?rev=11474&r1=11473&r2=11474&view=diff
==============================================================================
--- 1.3/test_suite/unit_tests/_maths_fns/test_frame_order_matrix_ops.py
(original)
+++ 1.3/test_suite/unit_tests/_maths_fns/test_frame_order_matrix_ops.py Wed
Aug 11 23:03:37 2010
@@ -811,6 +811,39 @@
self.assertAlmostEqual(f2a[i, j], f2b[i, j])
+ def test_compile_2nd_matrix_rotor(self):
+ """Check the operation of the compile_2nd_matrix_rotor() function."""
+
+ # The real 2nd degree frame order matrix.
+ real = array(
+ [[ 0.7069, -0.0002, 0, -0.0002,
0.2931, 0, 0, 0, 0],
+ [ 0.0002, 0.7069, 0, -0.2931,
-0.0002, 0, 0, 0, 0],
+ [ 0, 0, 0.8271, 0,
0, -0.0003, 0, 0, 0],
+ [ 0.0002, -0.2931, 0, 0.7069,
-0.0002, 0, 0, 0, 0],
+ [ 0.2931, 0.0002, 0, 0.0002,
0.7069, 0, 0, 0, 0],
+ [ 0, 0, 0.0003, 0,
0, 0.8271, 0, 0, 0],
+ [ 0, 0, 0, 0,
0, 0, 0.8271, -0.0003, 0],
+ [ 0, 0, 0, 0,
0, 0, 0.0003, 0.8271, 0],
+ [ 0, 0, 0, 0,
0, 0, 0, 0, 1.0000]])
+
+ # Init.
+ sigma_max = 60.0 / 180.0 * pi
+
+ # Calculate the matrix.
+ f2 = compile_2nd_matrix_rotor(self.f2_temp, self.R_temp,
self.z_axis, self.cone_axis, 0.0, 0.0, sigma_max)
+
+ # Print out.
+ print_frame_order_2nd_degree(real, "real")
+ print_frame_order_2nd_degree(f2, "calculated")
+ print_frame_order_2nd_degree(real-f2, "difference")
+
+ # Check the values.
+ for i in range(9):
+ for j in range(9):
+ print "Element %s, %s." % (i, j)
+ self.assert_(abs(f2[i, j] - real[i, j]) < 1e-3)
+
+
def test_reduce_alignment_tensor_order(self):
"""Test the alignment tensor reduction for the order identity
matrix."""
r11474 - in /1.3: maths_fns/ test_suite/unit_tests/_maths_fns/