Author: bugman
Date: Fri Aug 6 15:12:56 2010
New Revision: 11431
URL: http://svn.gna.org/viewcvs/relax?rev=11431&view=rev
Log:
The isotropic cone frame order model now uses the full eigenframe.
This is necessary to define the torsion angle restriction.
Modified:
1.3/maths_fns/frame_order.py
1.3/maths_fns/frame_order_matrix_ops.py
1.3/specific_fns/frame_order.py
Modified: 1.3/maths_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/maths_fns/frame_order.py?rev=11431&r1=11430&r2=11431&view=diff
==============================================================================
--- 1.3/maths_fns/frame_order.py (original)
+++ 1.3/maths_fns/frame_order.py Fri Aug 6 15:12:56 2010
@@ -220,10 +220,10 @@
"""
# Unpack the parameters.
- ave_pos_alpha, ave_pos_beta, ave_pos_gamma, axis_theta, axis_phi,
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, self.z_axis, self.cone_axis, axis_theta, axis_phi, cone_theta,
sigma_max)
+ 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)
# Reduce and rotate the tensors.
self.reduce_and_rot(ave_pos_alpha, ave_pos_beta, ave_pos_gamma,
frame_order_2nd)
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=11431&r1=11430&r2=11431&view=diff
==============================================================================
--- 1.3/maths_fns/frame_order_matrix_ops.py (original)
+++ 1.3/maths_fns/frame_order_matrix_ops.py Fri Aug 6 15:12:56 2010
@@ -60,7 +60,7 @@
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_iso_cone(matrix, R, z_axis, cone_axis, theta_axis,
phi_axis, cone_theta, sigma_max):
+def compile_2nd_matrix_iso_cone(matrix, R, eigen_alpha, eigen_beta,
eigen_gamma, cone_theta, sigma_max):
"""Generate the rotated 2nd degree Frame Order matrix for the isotropic
cone.
The cone axis is assumed to be parallel to the z-axis in the eigenframe.
@@ -69,28 +69,23 @@
@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 eigen_alpha: The eigenframe rotation alpha Euler angle.
+ @type eigen_alpha: float
+ @param eigen_beta: The eigenframe rotation beta Euler angle.
+ @type eigen_beta: float
+ @param eigen_gamma: The eigenframe rotation gamma Euler angle.
+ @type eigen_gamma: float
@param cone_theta: The cone opening angle.
@type cone_theta: float
@param sigma_max: The maximum torsion angle.
@type sigma_max: float
"""
- # Generate the cone axis from the spherical angles.
- spherical_to_cartesian([1.0, theta_axis, phi_axis], cone_axis)
-
# Populate the Frame Order matrix in the eigenframe.
populate_2nd_eigenframe_iso_cone(matrix, cone_theta, sigma_max)
# Average position rotation.
- two_vect_to_R(z_axis, cone_axis, R)
+ euler_to_R_zyz(eigen_alpha, eigen_beta, eigen_gamma, R)
# Rotate and return the frame order matrix.
return rotate_daeg(matrix, R)
Modified: 1.3/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/frame_order.py?rev=11431&r1=11430&r2=11431&view=diff
==============================================================================
--- 1.3/specific_fns/frame_order.py (original)
+++ 1.3/specific_fns/frame_order.py Fri Aug 6 15:12:56 2010
@@ -91,13 +91,13 @@
param_vect = [cdp.ave_pos_alpha, cdp.ave_pos_beta,
cdp.ave_pos_gamma]
# Frame order eigenframe - the full frame.
- if cdp.model in ['pseudo-ellipse', 'pseudo-ellipse, torsionless',
'pseudo-ellipse, free rotor']:
+ if cdp.model in ['iso cone', 'pseudo-ellipse', 'pseudo-ellipse,
torsionless', 'pseudo-ellipse, free rotor']:
param_vect.append(cdp.eigen_alpha)
param_vect.append(cdp.eigen_beta)
param_vect.append(cdp.eigen_gamma)
# Frame order eigenframe - the isotropic cone axis.
- elif cdp.model in ['iso cone', 'iso cone, torsionless', 'iso cone,
free rotor']:
+ elif cdp.model in ['iso cone, torsionless', 'iso cone, free rotor']:
param_vect.append(cdp.axis_theta)
param_vect.append(cdp.axis_phi)
@@ -505,13 +505,13 @@
cdp.params.append('ave_pos_gamma')
# Frame order eigenframe - the full frame.
- if cdp.model in ['pseudo-ellipse', 'pseudo-ellipse,
torsionless', 'pseudo-ellipse, free rotor']:
+ if cdp.model in ['iso cone', 'pseudo-ellipse', 'pseudo-ellipse,
torsionless', 'pseudo-ellipse, free rotor']:
cdp.params.append('eigen_alpha')
cdp.params.append('eigen_beta')
cdp.params.append('eigen_gamma')
# Frame order eigenframe - the isotropic cone axis.
- elif cdp.model in ['iso cone', 'iso cone, torsionless', 'iso
cone, free rotor']:
+ elif cdp.model in ['iso cone, torsionless', 'iso cone, free
rotor']:
cdp.params.append('axis_theta')
cdp.params.append('axis_phi')
@@ -575,7 +575,7 @@
elif cdp.model in ['pseudo-ellipse, torsionless', 'pseudo-ellipse,
free rotor']:
ave_pos_alpha, ave_pos_beta, ave_pos_gamma, eigen_alpha,
eigen_beta, eigen_gamma, cone_theta_x, cone_theta_y = param_vector
elif cdp.model == 'iso cone':
- ave_pos_alpha, ave_pos_beta, ave_pos_gamma, axis_theta,
axis_phi, cone_theta, cone_sigma_max = param_vector
+ ave_pos_alpha, ave_pos_beta, ave_pos_gamma, eigen_alpha,
eigen_beta, eigen_gamma, cone_theta, cone_sigma_max = param_vector
elif cdp.model in ['iso cone, torsionless', 'iso cone, free rotor']:
ave_pos_beta, ave_pos_gamma, axis_theta, axis_phi, cone_s1 =
param_vector
ave_pos_alpha = 0.0
@@ -790,13 +790,13 @@
names.append('ave_pos_gamma%s' % suffix)
# Frame order eigenframe - the full frame.
- if cdp.model in ['pseudo-ellipse', 'pseudo-ellipse,
torsionless', 'pseudo-ellipse, free rotor']:
+ if cdp.model in ['iso cone', 'pseudo-ellipse', 'pseudo-ellipse,
torsionless', 'pseudo-ellipse, free rotor']:
names.append('eigen_alpha%s' % suffix)
names.append('eigen_beta%s' % suffix)
names.append('eigen_gamma%s' % suffix)
# Frame order eigenframe - the isotropic cone axis.
- elif cdp.model in ['iso cone', 'iso cone, torsionless', 'iso
cone, free rotor']:
+ elif cdp.model in ['iso cone, torsionless', 'iso cone, free
rotor']:
names.append('axis_theta%s' % suffix)
names.append('axis_phi%s' % suffix)
r11431 - in /1.3: maths_fns/frame_order.py maths_fns/frame_order_matrix_ops.py specific_fns/frame_order.py