Author: bugman
Date: Tue Dec 6 11:53:10 2011
New Revision: 15036
URL: http://svn.gna.org/viewcvs/relax?rev=15036&view=rev
Log:
Renamed the rotation matrices in the frame order target functions to be more
logical.
Modified:
branches/frame_order_testing/maths_fns/frame_order.py
branches/frame_order_testing/maths_fns/frame_order_matrix_ops.py
Modified: branches/frame_order_testing/maths_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/maths_fns/frame_order.py?rev=15036&r1=15035&r2=15036&view=diff
==============================================================================
--- branches/frame_order_testing/maths_fns/frame_order.py (original)
+++ branches/frame_order_testing/maths_fns/frame_order.py Tue Dec 6 11:53:10
2011
@@ -293,8 +293,9 @@
self.A_5D_bc = zeros(self.num_tensors*5, float64)
# The rotation to the Frame Order eigenframe.
- self.rot = zeros((3, 3), float64)
- self.rot2 = zeros((3, 3), float64)
+ self.R_eigen = zeros((3, 3), float64)
+ self.R_ave = zeros((3, 3), float64)
+ self.Ri_prime = zeros((3, 3), float64)
self.tensor_3D = zeros((3, 3), float64)
# The cone axis storage and molecular frame z-axis.
@@ -320,7 +321,7 @@
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)
+ frame_order_2nd =
compile_2nd_matrix_free_rotor(self.frame_order_2nd, self.R_eigen,
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)
@@ -346,7 +347,7 @@
theta, phi, theta_cone = params
# Generate the 2nd degree Frame Order super matrix.
- self.frame_order_2nd =
compile_2nd_matrix_iso_cone_free_rotor(self.frame_order_2nd, self.rot,
self.z_axis, self.cone_axis, theta, phi, theta_cone)
+ self.frame_order_2nd =
compile_2nd_matrix_iso_cone_free_rotor(self.frame_order_2nd, self.R_eigen,
self.z_axis, self.cone_axis, theta, phi, theta_cone)
# Make the Frame Order matrix contiguous.
self.frame_order_2nd = self.frame_order_2nd.copy()
@@ -383,7 +384,7 @@
ave_pos_alpha, ave_pos_beta, ave_pos_gamma, eigen_alpha, eigen_beta,
eigen_gamma, cone_theta, sigma_max = params
# Generate the 2nd degree Frame Order super matrix.
- frame_order_2nd = compile_2nd_matrix_iso_cone(self.frame_order_2nd,
self.rot, eigen_alpha, eigen_beta, eigen_gamma, cone_theta, sigma_max)
+ frame_order_2nd = compile_2nd_matrix_iso_cone(self.frame_order_2nd,
self.R_eigen, eigen_alpha, eigen_beta, eigen_gamma, cone_theta, sigma_max)
# Reduce and rotate the tensors.
self.reduce_and_rot(ave_pos_alpha, ave_pos_beta, ave_pos_gamma,
frame_order_2nd)
@@ -407,7 +408,7 @@
ave_pos_beta, ave_pos_gamma, axis_theta, axis_phi, cone_s1 = params
# Generate the 2nd degree Frame Order super matrix.
- frame_order_2nd =
compile_2nd_matrix_iso_cone_free_rotor(self.frame_order_2nd, self.rot,
self.z_axis, self.cone_axis, axis_theta, axis_phi, cone_s1)
+ frame_order_2nd =
compile_2nd_matrix_iso_cone_free_rotor(self.frame_order_2nd, self.R_eigen,
self.z_axis, self.cone_axis, axis_theta, axis_phi, cone_s1)
# Reduce and rotate the tensors.
self.reduce_and_rot(0.0, ave_pos_beta, ave_pos_gamma,
frame_order_2nd)
@@ -431,7 +432,7 @@
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)
+ frame_order_2nd =
compile_2nd_matrix_iso_cone_torsionless(self.frame_order_2nd, self.R_eigen,
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)
@@ -453,7 +454,7 @@
ave_pos_alpha, ave_pos_beta, ave_pos_gamma, eigen_alpha, eigen_beta,
eigen_gamma, cone_theta_x, cone_theta_y, cone_sigma_max = params
# Generate the 2nd degree Frame Order super matrix.
- frame_order_2nd =
compile_2nd_matrix_pseudo_ellipse(self.frame_order_2nd, self.rot,
eigen_alpha, eigen_beta, eigen_gamma, cone_theta_x, cone_theta_y,
cone_sigma_max)
+ frame_order_2nd =
compile_2nd_matrix_pseudo_ellipse(self.frame_order_2nd, self.R_eigen,
eigen_alpha, eigen_beta, eigen_gamma, cone_theta_x, cone_theta_y,
cone_sigma_max)
# Reduce and rotate the tensors.
self.reduce_and_rot(ave_pos_alpha, ave_pos_beta, ave_pos_gamma,
frame_order_2nd)
@@ -475,7 +476,7 @@
ave_pos_alpha, ave_pos_beta, ave_pos_gamma, eigen_alpha, eigen_beta,
eigen_gamma, cone_theta_x, cone_theta_y = params
# Generate the 2nd degree Frame Order super matrix.
- frame_order_2nd =
compile_2nd_matrix_pseudo_ellipse_free_rotor(self.frame_order_2nd, self.rot,
eigen_alpha, eigen_beta, eigen_gamma, cone_theta_x, cone_theta_y)
+ frame_order_2nd =
compile_2nd_matrix_pseudo_ellipse_free_rotor(self.frame_order_2nd,
self.R_eigen, eigen_alpha, eigen_beta, eigen_gamma, cone_theta_x,
cone_theta_y)
# Reduce and rotate the tensors.
self.reduce_and_rot(ave_pos_alpha, ave_pos_beta, ave_pos_gamma,
frame_order_2nd)
@@ -497,7 +498,7 @@
ave_pos_alpha, ave_pos_beta, ave_pos_gamma, eigen_alpha, eigen_beta,
eigen_gamma, cone_theta_x, cone_theta_y = params
# Generate the 2nd degree Frame Order super matrix.
- frame_order_2nd =
compile_2nd_matrix_pseudo_ellipse_torsionless(self.frame_order_2nd, self.rot,
eigen_alpha, eigen_beta, eigen_gamma, cone_theta_x, cone_theta_y)
+ frame_order_2nd =
compile_2nd_matrix_pseudo_ellipse_torsionless(self.frame_order_2nd,
self.R_eigen, eigen_alpha, eigen_beta, eigen_gamma, cone_theta_x,
cone_theta_y)
# Reduce and rotate the tensors.
self.reduce_and_rot(ave_pos_alpha, ave_pos_beta, ave_pos_gamma,
frame_order_2nd)
@@ -553,7 +554,7 @@
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)
+ frame_order_2nd = compile_2nd_matrix_rotor(self.frame_order_2nd,
self.R_eigen, 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)
@@ -570,7 +571,10 @@
for j in xrange(self.num_pcs):
# The back calculated PCS.
if self.pcs_flag and not self.missing_pcs[i, j]:
- self.pcs_theta[i, j] =
pcs_numeric_int_rotor(axis_theta=axis_theta, axis_phi=axis_phi,
sigma_max=sigma_max, c=self.pcs_const[i], atom_pos=self.pcs_atoms[j],
pivot=pivot, ln_pos=self.paramag_centre, A=self.A_3D[i], ave_pos_R=self.rot,
R=)
+ if self.full_in_ref_frame[i]:
+ self.pcs_theta[i, j] =
pcs_numeric_int_rotor(axis_theta=axis_theta, axis_phi=axis_phi,
sigma_max=sigma_max, c=self.pcs_const[i], atom_pos=self.pcs_atoms[j],
pivot=pivot, ln_pos=self.paramag_centre, A=self.A_3D[i],
ave_pos_R=self.R_ave, R=self.Ri_prime)
+ else:
+ self.pcs_theta[i, j] =
pcs_numeric_int_rotor(axis_theta=axis_theta, axis_phi=axis_phi,
sigma_max=sigma_max, c=self.pcs_const[i], atom_pos=self.pcs_atoms[j],
pivot=pivot, ln_pos=self.paramag_centre, A=self.A_3D[i],
ave_pos_R=transpose(self.R_ave), R=self.Ri_prime)
# Calculate and sum the single alignment chi-squared value (for
the RDC).
if self.rdc_flag:
@@ -598,7 +602,7 @@
"""
# Alignment tensor rotation.
- euler_to_R(ave_pos_alpha, ave_pos_beta, ave_pos_gamma, self.rot)
+ euler_to_R(ave_pos_alpha, ave_pos_beta, ave_pos_gamma, self.R_ave)
# Back calculate the rotated tensors.
for i in range(self.num_tensors):
@@ -621,11 +625,11 @@
# Rotate the tensor (normal R.X.RT rotation).
if self.full_in_ref_frame[i]:
- self.A_3D_bc[i] = dot(self.rot, dot(self.tensor_3D,
transpose(self.rot)))
+ self.A_3D_bc[i] = dot(self.R_ave, dot(self.tensor_3D,
transpose(self.R_ave)))
# Rotate the tensor (inverse RT.X.R rotation).
else:
- self.A_3D_bc[i] = dot(transpose(self.rot),
dot(self.tensor_3D, self.rot))
+ self.A_3D_bc[i] = dot(transpose(self.R_ave),
dot(self.tensor_3D, self.R_ave))
# Convert the tensor back to 5D, rank-1 form, as the
back-calculated reduced tensor.
to_5D(self.A_5D_bc[index1:index2], self.A_3D_bc[i])
Modified: branches/frame_order_testing/maths_fns/frame_order_matrix_ops.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/maths_fns/frame_order_matrix_ops.py?rev=15036&r1=15035&r2=15036&view=diff
==============================================================================
--- branches/frame_order_testing/maths_fns/frame_order_matrix_ops.py
(original)
+++ branches/frame_order_testing/maths_fns/frame_order_matrix_ops.py Tue Dec
6 11:53:10 2011
@@ -1312,7 +1312,7 @@
return 2 - 2*cos(tmax)**3
-def pcs_numeric_int_rotor(axis_theta=None, axis_phi=None, sigma_max=None,
c=None, atom_pos=None, pivot=None, ln_pos=None, A=None, ave_pos_R=None,
R=None):
+def pcs_numeric_int_rotor(axis_theta=None, axis_phi=None, sigma_max=None,
c=None, atom_pos=None, pivot=None, ln_pos=None, A=None, ave_pos_R=None,
Ri=None):
"""Determine the averaged PCS value via numerical integration.
@keyword axis_theta: The rotation axis polar angle.
@@ -1333,23 +1333,23 @@
@type A: numpy rank-2, 3D array
@keyword ave_pos_R: The rotation matrix for rotating from the
reference frame to the average position.
@type ave_pos_R: numpy rank-2, 3D array
- @keyword R: The empty rotation matrix for the in-frame rotor
motion.
- @type R: numpy rank-2, 3D array
+ @keyword Ri: The empty rotation matrix for the in-frame rotor
motion, used to calculate the PCS for each state i in the numerical
integration.
+ @type Ri: numpy rank-2, 3D array
@return: The averaged PCS value.
@rtype: float
"""
- # Preset the rotation matrix elements.
- R[0, 2] = 0.0
- R[1, 2] = 0.0
- R[2, 0] = 0.0
- R[2, 1] = 0.0
- R[2, 2] = 1.0
+ # Preset the rotation matrix elements for state i.
+ Ri[0, 2] = 0.0
+ Ri[1, 2] = 0.0
+ Ri[2, 0] = 0.0
+ Ri[2, 1] = 0.0
+ Ri[2, 2] = 1.0
# Convert the PCS constant to Angstrom units.
c = c * 1e30
- # Perform triple numerical integration.
+ # Perform numerical integration.
result = quad(pcs_pivot_motion_rotor, -sigma_max, sigma_max, args=(c,
atom_pos, pivot, ln_pos, A, R), full_output=1)
# The surface area normalisation factor.
@@ -1359,11 +1359,11 @@
return result[0] / SA
-def pcs_pivot_motion_rotor(sigma, c, pN, pPiv, pLn, A, R):
+def pcs_pivot_motion_rotor(sigma_i, c, pN, pPiv, pLn, A, Ri):
"""Calculate the PCS value after a pivoted motion for the rotor model.
- @param sigma: The rotor angle.
- @type sigma: float
+ @param sigma_i: The rotor angle for state i.
+ @type sigma_i: float
@param c: The PCS constant (without the interatomic distance).
@type c: float
@param pN: The Euclidean position of the atom of interest.
@@ -1374,15 +1374,15 @@
@type pLn: numpy rank-1, 3D array
@param A: The full alignment tensor of the non-moving domain.
@type A: numpy rank-2, 3D array
- @param R: The empty rotation matrix for the in-frame rotor motion.
- @type R: numpy rank-2, 3D array
+ @param Ri: The empty rotation matrix for the in-frame rotor motion
for state i.
+ @type Ri: numpy rank-2, 3D array
@return: The PCS value for the changed position.
@rtype: float
"""
# The rotation matrix.
- c_sigma = cos(sigma)
- s_sigma = sin(sigma)
+ c_sigma = cos(sigma_i)
+ s_sigma = sin(sigma_i)
R[0, 0] = c_sigma
R[0, 1] = -s_sigma
R[1, 0] = s_sigma
r15036 - in /branches/frame_order_testing/maths_fns: frame_order.py frame_order_matrix_ops.py