Author: bugman
Date: Tue Jun 23 11:14:13 2009
New Revision: 9128
URL: http://svn.gna.org/viewcvs/relax?rev=9128&view=rev
Log:
Elimination of an Euler angle from the isotropic cone model.
Only the cone axis theta and phi angles are now optimised.
Modified:
branches/frame_order/maths_fns/frame_order_models.py
branches/frame_order/specific_fns/frame_order.py
Modified: branches/frame_order/maths_fns/frame_order_models.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order/maths_fns/frame_order_models.py?rev=9128&r1=9127&r2=9128&view=diff
==============================================================================
--- branches/frame_order/maths_fns/frame_order_models.py (original)
+++ branches/frame_order/maths_fns/frame_order_models.py Tue Jun 23 11:14:13
2009
@@ -152,12 +152,11 @@
def func_iso_cone(self, params):
"""Target function for isotropic cone model optimisation using the
alignment tensors.
- This function optimises against alignment tensors. The Frame Order
eigenframe via the
- alpha, beta, and gamma Euler angles, and the cone angle theta are
the 4 parameters optimised
- in this model.
-
- @param params: The vector of parameter values {alpha, beta, gamma,
theta} where the first
- three are the Euler angles for the Frame Order
eigenframe and theta is the
+ This function optimises against alignment tensors. The cone axis
spherical angles theta and
+ phi and the cone angle theta are the 3 parameters optimised in this
model.
+
+ @param params: The vector of parameter values {theta, phi,
theta_cone} where the first two
+ are the polar and azimuthal angles of the cone axis
theta_cone is the
isotropic cone angle.
@type params: list of float
@return: The chi-squared or SSE value.
@@ -165,10 +164,10 @@
"""
# Break up the parameters.
- alpha, beta, gamma, theta = params
+ theta, phi, theta_cone = params
# Generate the 2nd degree Frame Order super matrix.
- self.frame_order_2nd =
compile_2nd_matrix_iso_cone(self.frame_order_2nd, self.rot, alpha, beta,
gamma, theta)
+ self.frame_order_2nd =
compile_2nd_matrix_iso_cone(self.frame_order_2nd, self.rot, self.z_axis,
theta, phi, theta_cone)
# Back calculate the reduced tensors.
for i in range(self.num_tensors):
@@ -182,11 +181,11 @@
"""Target function for isotropic cone model optimisation using the
Frame Order matrix.
This function optimises by directly matching the elements of the 2nd
degree Frame Order
- super matrix. The Frame Order eigenframe via the alpha, beta, and
gamma Euler angles, and
- the cone angle theta are the 4 parameters optimised in this model.
-
- @param params: The vector of parameter values {alpha, beta, gamma,
theta} where the first
- three are the Euler angles for the Frame Order
eigenframe and theta is the
+ super matrix. The cone axis spherical angles theta and phi and the
cone angle theta are the
+ 3 parameters optimised in this model.
+
+ @param params: The vector of parameter values {theta, phi,
theta_cone} where the first two
+ are the polar and azimuthal angles of the cone axis
theta_cone is the
isotropic cone angle.
@type params: list of float
@return: The chi-squared or SSE value.
@@ -194,10 +193,10 @@
"""
# Break up the parameters.
- alpha, beta, gamma, theta = params
+ theta, phi, theta_cone = params
# Generate the 2nd degree Frame Order super matrix.
- self.frame_order_2nd =
compile_2nd_matrix_iso_cone(self.frame_order_2nd, self.rot, alpha, beta,
gamma, theta)
+ self.frame_order_2nd =
compile_2nd_matrix_iso_cone(self.frame_order_2nd, self.rot, self.z_axis,
theta, phi, theta_cone)
# Make the Frame Order matrix contiguous.
self.frame_order_2nd = self.frame_order_2nd.copy()
Modified: branches/frame_order/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order/specific_fns/frame_order.py?rev=9128&r1=9127&r2=9128&view=diff
==============================================================================
--- branches/frame_order/specific_fns/frame_order.py (original)
+++ branches/frame_order/specific_fns/frame_order.py Tue Jun 23 11:14:13 2009
@@ -105,20 +105,17 @@
if cdp.model == 'iso cone':
# Set up the parameter arrays.
if not len(cdp.params):
- cdp.params.append('alpha')
- cdp.params.append('beta')
- cdp.params.append('gamma')
- cdp.params.append('theta')
-
- # Initialise the Euler angle and cone angle values.
- if not hasattr(cdp, 'alpha'):
- cdp.alpha = 0.0
- if not hasattr(cdp, 'beta'):
- cdp.beta = 0.0
- if not hasattr(cdp, 'gamma'):
- cdp.gamma = 0.0
- if not hasattr(cdp, 'theta'):
- cdp.theta = 0.0
+ cdp.params.append('theta_axis')
+ cdp.params.append('phi_axis')
+ cdp.params.append('theta_cone')
+
+ # Initialise the cone axis angles and cone angle values.
+ if not hasattr(cdp, 'theta_axis'):
+ cdp.theta_axis = 0.0
+ if not hasattr(cdp, 'phi_axis'):
+ cdp.phi_axis = 0.0
+ if not hasattr(cdp, 'theta_cone'):
+ cdp.theta_cone = 0.0
def __unpack_opt_results(self, results, sim_index=None):
@@ -148,21 +145,20 @@
# Isotropic cone model.
if cdp.model == 'iso cone':
# Disassemble the parameter vector.
- alpha, beta, gamma, theta = param_vector
+ theta_axis, phi_axis, theta_cone = param_vector
# Wrap the cone angle to be between 0 and pi.
- if theta < 0.0:
- theta = -theta
- if theta > pi:
- theta = 2.0*pi - theta
+ if theta_cone < 0.0:
+ theta_cone = -theta_cone
+ if theta_cone > pi:
+ theta_cone = 2.0*pi - theta_cone
# Monte Carlo simulation data structures.
if sim_index != None:
# Model parameters.
- cdp.alpha_sim[sim_index] = alpha
- cdp.beta_sim[sim_index] = beta
- cdp.gamma_sim[sim_index] = gamma
- cdp.theta_sim[sim_index] = theta
+ cdp.theta_axis_sim[sim_index] = theta_axis
+ cdp.phi_axis_sim[sim_index] = phi_axis
+ cdp.theta_cone_sim[sim_index] = theta_cone
# Optimisation info.
cdp.chi2_sim[sim_index] = func
@@ -175,10 +171,9 @@
# Normal data structures.
else:
# Model parameters.
- cdp.alpha = alpha
- cdp.beta = beta
- cdp.gamma = gamma
- cdp.theta = theta
+ cdp.theta_axis = theta_axis
+ cdp.phi_axis = phi_axis
+ cdp.theta_cone = theta_cone
# Optimisation info.
cdp.chi2 = func
@@ -232,14 +227,12 @@
# Set the grid search options.
for i in xrange(n):
- # Euler angles.
- if cdp.params[i] in ['alpha', 'gamma']:
- grid_ops.append([inc[i], 0.0, 2*pi])
- if cdp.params[i] == 'beta':
+ # Cone axis angles and cone angle.
+ if cdp.params[i] == 'phi_axis':
grid_ops.append([inc[i], 0.0, pi])
-
- # The cone angle.
- if cdp.params[i] == 'theta':
+ if cdp.params[i] == 'theta_axis':
+ grid_ops.append([inc[i], 0.0, pi])
+ if cdp.params[i] == 'theta_cone':
grid_ops.append([inc[i], 0.0, pi])
# Lower bound (if supplied).
@@ -287,8 +280,8 @@
# Isotropic cone model.
if cdp.model == 'iso cone':
- # The initial parameter vector (the Euler angles and the cone
angle).
- param_vector = array([cdp.alpha, cdp.beta, cdp.gamma,
cdp.theta], float64)
+ # The initial parameter vector (the cone axis angles and the
cone angle).
+ param_vector = array([cdp.theta_axis, cdp.phi_axis,
cdp.theta_cone], float64)
# Get the data structures for optimisation using the tensors as
base data sets.
full_tensors, red_tensors, red_tensor_err =
self.__minimise_setup_tensors()
r9128 - in /branches/frame_order: maths_fns/frame_order_models.py specific_fns/frame_order.py