Author: bugman
Date: Wed Jan 13 15:15:37 2010
New Revision: 10197
URL: http://svn.gna.org/viewcvs/relax?rev=10197&view=rev
Log:
Removed the alpha Euler angle from the isotropic code frame order model.
Modified:
1.3/maths_fns/frame_order.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=10197&r1=10196&r2=10197&view=diff
==============================================================================
--- 1.3/maths_fns/frame_order.py (original)
+++ 1.3/maths_fns/frame_order.py Wed Jan 13 15:15:37 2010
@@ -225,26 +225,22 @@
def func_iso_cone(self, params):
"""Target function for isotropic cone model optimisation using the
alignment tensors.
- 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 {alpha, beta, gamma,
theta, phi, theta_cone}
- where the first 3 are the tensor rotation Euler
angles, the next two are the
- polar and azimuthal angles of the cone axis
theta_cone is the isotropic cone
- angle.
+ This function optimises against alignment tensors.
+
+ @param params: The vector of parameter values {beta, gamma, theta,
phi, theta_cone} where the first 2 are the tensor rotation Euler angles, the
next 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.
@rtype: float
"""
# Unpack the parameters.
- alpha, beta, gamma, theta, phi, theta_cone = params
+ beta, gamma, 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, self.z_axis,
self.cone_axis, theta, phi, theta_cone)
# Reduced alignment tensor rotation.
- euler_to_R(alpha, beta, gamma, self.rot)
+ euler_to_R(0.0, beta, gamma, self.rot)
# Back calculate the reduced tensors.
for i in range(self.num_tensors):
Modified: 1.3/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/frame_order.py?rev=10197&r1=10196&r2=10197&view=diff
==============================================================================
--- 1.3/specific_fns/frame_order.py (original)
+++ 1.3/specific_fns/frame_order.py Wed Jan 13 15:15:37 2010
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2009 Edward d'Auvergne
#
+# Copyright (C) 2009-2010 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -73,7 +73,7 @@
# The isotropic cone model initial parameter vector (the cone axis
angles and the cone angle).
elif cdp.model == 'iso cone':
- return array([cdp.alpha, cdp.beta, cdp.gamma, cdp.theta_axis,
cdp.phi_axis, cdp.theta_cone], float64)
+ return array([cdp.beta, cdp.gamma, cdp.theta_axis, cdp.phi_axis,
cdp.theta_cone], float64)
def _back_calc(self):
@@ -433,9 +433,13 @@
# Set up the tensor rotation parameter arrays.
if init:
- cdp.params.append('alpha')
- cdp.params.append('beta')
- cdp.params.append('gamma')
+ if cdp.model == 'iso cone':
+ cdp.params.append('beta')
+ cdp.params.append('gamma')
+ else:
+ cdp.params.append('alpha')
+ cdp.params.append('beta')
+ cdp.params.append('gamma')
# Initialise the tensor rotation angles.
if not hasattr(cdp, 'alpha'):
@@ -497,7 +501,10 @@
# Isotropic cone model.
elif cdp.model == 'iso cone':
# Disassemble the parameter vector.
- alpha, beta, gamma, theta_axis, phi_axis, theta_cone =
param_vector
+ beta, gamma, theta_axis, phi_axis, theta_cone = param_vector
+
+ # Alpha is zero in this model!
+ alpha = 0.0
# Wrap the cone angle to be between 0 and pi.
if theta_cone < 0.0:
@@ -667,15 +674,22 @@
# Parameters.
if set == 'all' or set == 'params':
- names.append('alpha')
- names.append('beta')
- names.append('gamma')
-
# The isotropic cone model.
if hasattr(cdp, 'model') and cdp.model == 'iso cone':
+ # Euler angles.
+ names.append('beta')
+ names.append('gamma')
+
+ # Angular cone parameters.
names.append('theta_axis')
names.append('phi_axis')
names.append('theta_cone')
+
+ # All other models.
+ else:
+ names.append('alpha')
+ names.append('beta')
+ names.append('gamma')
# Minimisation statistics.
if set == 'all' or set == 'min':
@@ -688,27 +702,41 @@
# Parameter errors.
if error_names and (set == 'all' or set == 'params'):
- names.append('alpha_err')
- names.append('beta_err')
- names.append('gamma_err')
-
# The isotropic cone model.
if hasattr(cdp, 'model') and cdp.model == 'iso cone':
+ # Euler angles.
+ names.append('beta_err')
+ names.append('gamma_err')
+
+ # Angular cone parameters.
names.append('theta_axis_err')
names.append('phi_axis_err')
names.append('theta_cone_err')
+ # All other models.
+ else:
+ names.append('alpha_err')
+ names.append('beta_err')
+ names.append('gamma_err')
+
# Parameter simulation values.
if sim_names and (set == 'all' or set == 'params'):
- names.append('alpha_sim')
- names.append('beta_sim')
- names.append('gamma_sim')
-
# The isotropic cone model.
if hasattr(cdp, 'model') and cdp.model == 'iso cone':
+ # Euler angles.
+ names.append('beta_sim')
+ names.append('gamma_sim')
+
+ # Angular cone parameters.
names.append('theta_axis_sim')
names.append('phi_axis_sim')
names.append('theta_cone_sim')
+
+ # All other models.
+ else:
+ names.append('alpha_sim')
+ names.append('beta_sim')
+ names.append('gamma_sim')
# Return the names.
return names
r10197 - in /1.3: maths_fns/frame_order.py specific_fns/frame_order.py