Author: bugman
Date: Tue Feb 2 00:19:55 2010
New Revision: 10612
URL: http://svn.gna.org/viewcvs/relax?rev=10612&view=rev
Log:
Switched from using a cone angle to using an order parameter in the isotropic
cone frame order model.
Modified:
1.3/maths_fns/__init__.py
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/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/maths_fns/__init__.py?rev=10612&r1=10611&r2=10612&view=diff
==============================================================================
--- 1.3/maths_fns/__init__.py (original)
+++ 1.3/maths_fns/__init__.py Tue Feb 2 00:19:55 2010
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2005, 2008-2009 Edward d'Auvergne
#
+# Copyright (C) 2003-2005, 2008-2010 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -37,6 +37,7 @@
'kronecker_product',
'mf',
'n_state_model',
+ 'order_parameters',
'pcs',
'potential',
'rdc',
Modified: 1.3/maths_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/maths_fns/frame_order.py?rev=10612&r1=10611&r2=10612&view=diff
==============================================================================
--- 1.3/maths_fns/frame_order.py (original)
+++ 1.3/maths_fns/frame_order.py Tue Feb 2 00:19:55 2010
@@ -227,17 +227,17 @@
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.
+ @param params: The vector of parameter values {beta, gamma, theta,
phi, s1} where the first 2 are the tensor rotation Euler angles, the next two
are the polar and azimuthal angles of the cone axis, and s1 is the isotropic
cone order parameter.
@type params: list of float
@return: The chi-squared or SSE value.
@rtype: float
"""
# Unpack the parameters.
- beta, gamma, theta, phi, theta_cone = params
+ beta, gamma, theta, phi, s1 = 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)
+ self.frame_order_2nd =
compile_2nd_matrix_iso_cone(self.frame_order_2nd, self.rot, self.z_axis,
self.cone_axis, theta, phi, s1)
# Reduced alignment tensor rotation.
euler_to_R(0.0, beta, gamma, self.rot)
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=10612&r1=10611&r2=10612&view=diff
==============================================================================
--- 1.3/maths_fns/frame_order_matrix_ops.py (original)
+++ 1.3/maths_fns/frame_order_matrix_ops.py Tue Feb 2 00:19:55 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.
#
#
#
@@ -30,12 +30,19 @@
# relax module imports.
from float import isNaN
+from maths_fns import order_parameters
from maths_fns.kronecker_product import kron_prod, transpose_23
from maths_fns.rotation_matrix import two_vect_to_R
-def compile_2nd_matrix_iso_cone(matrix, R, z_axis, cone_axis, theta_axis,
phi_axis, theta_cone):
+def compile_2nd_matrix_iso_cone(matrix, R, z_axis, cone_axis, theta_axis,
phi_axis, s1):
"""Generate the rotated 2nd degree Frame Order matrix.
+
+ The cone axis is assumed to be parallel to the z-axis in the eigenframe.
In this model, the three order parameters are defined as::
+
+ S1 = S2,
+ S3 = 0
+
@param matrix: The Frame Order matrix, 2nd degree to be populated.
@type matrix: numpy 9D, rank-2 array
@@ -49,8 +56,8 @@
@type theta_axis: float
@param phi_axis: The cone axis azimuthal angle.
@type phi_axis: float
- @param theta_cone: The cone angle in radians.
- @type theta_cone: float
+ @param s1: The cone order parameter.
+ @type s1: float
"""
# Generate the cone axis from the spherical angles.
@@ -63,7 +70,7 @@
R_kron = kron_prod(R, R)
# Populate the Frame Order matrix in the eigenframe.
- populate_2nd_eigenframe_iso_cone(matrix, theta_cone)
+ populate_2nd_eigenframe_iso_cone(matrix, s1)
# Perform the T23 transpose to obtain the Kronecker product matrix!
transpose_23(matrix)
@@ -170,15 +177,19 @@
matrix[2, 2] = (cos(angle) + 1.0) / 2.0
-def populate_2nd_eigenframe_iso_cone(matrix, angle):
+def populate_2nd_eigenframe_iso_cone(matrix, s1):
"""Populate the 2nd degree Frame Order matrix in the eigenframe for an
isotropic cone.
- The cone axis is assumed to be parallel to the z-axis in the eigenframe.
+ The cone axis is assumed to be parallel to the z-axis in the eigenframe.
In this model, the three order parameters are defined as::
+
+ S1 = S2,
+ S3 = 0
+
@param matrix: The Frame Order matrix, 2nd degree.
@type matrix: numpy 9D, rank-2 array
- @param angle: The cone angle.
- @type angle: float
+ @param s1: The cone order parameter.
+ @type s1: float
"""
# Zeros.
@@ -186,24 +197,23 @@
for j in range(9):
matrix[i, j] = 0.0
- # Trigonometric terms.
- cos_theta = cos(angle)
- cos2_theta = cos_theta**2
-
# The c11^2, c22^2, c12^2, and c21^2 elements.
- matrix[0, 0] = (4.0 + cos_theta + cos2_theta) / 12.0
+ matrix[0, 0] = (s1 + 1.0) / 3.0
matrix[4, 4] = matrix[0, 0]
matrix[1, 1] = matrix[0, 0]
matrix[3, 3] = matrix[0, 0]
# The c33^2 element.
- matrix[8, 8] = (1.0 + cos_theta + cos2_theta) / 3.0
+ matrix[8, 8] = (2.0*s1 + 1.0) / 3.0
# The c13^2, c31^2, c23^2, c32^2 elements.
- matrix[2, 2] = (2.0 + cos_theta)*(1.0 - cos_theta) / 6.0
+ matrix[2, 2] = (1.0 - s1) / 3.0
matrix[6, 6] = matrix[2, 2]
matrix[5, 5] = matrix[2, 2]
matrix[7, 7] = matrix[2, 2]
+
+ # Calculate the cone angle.
+ cos_theta = order_parameters.cos_theta(s1)
# The c11.c22 and c12.c21 elements.
matrix[0, 4] = matrix[4, 0] = (cos_theta + 1.0) / 4.0
Modified: 1.3/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/frame_order.py?rev=10612&r1=10611&r2=10612&view=diff
==============================================================================
--- 1.3/specific_fns/frame_order.py (original)
+++ 1.3/specific_fns/frame_order.py Tue Feb 2 00:19:55 2010
@@ -40,7 +40,7 @@
from generic_fns.angles import wrap_angles
from generic_fns.structure.geometric import cone_edge, generate_vector_dist,
generate_vector_residues, stitch_cone_to_edge
from generic_fns.structure.internal import Internal
-from maths_fns import frame_order
+from maths_fns import frame_order, order_parameters
from maths_fns.frame_order_matrix_ops import generate_vector
from maths_fns.rotation_matrix import two_vect_to_R
from relax_errors import RelaxError, RelaxInfError, RelaxNaNError,
RelaxNoModelError
@@ -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.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.s1], float64)
def _back_calc(self):
@@ -455,15 +455,15 @@
if init:
cdp.params.append('theta_axis')
cdp.params.append('phi_axis')
- cdp.params.append('theta_cone')
-
- # Initialise the cone axis angles and cone angle values.
+ cdp.params.append('s1')
+
+ # Initialise the cone axis angles and order parameter 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
+ if not hasattr(cdp, 's1'):
+ cdp.s1 = 0.0
def _unpack_opt_results(self, results, sim_index=None):
@@ -501,30 +501,27 @@
# Isotropic cone model.
elif cdp.model == 'iso cone':
# Disassemble the parameter vector.
- beta, gamma, theta_axis, phi_axis, theta_cone = param_vector
+ beta, gamma, theta_axis, phi_axis, s1 = 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:
- theta_cone = -theta_cone
- if theta_cone > pi:
- theta_cone = 2.0*pi - theta_cone
+ # Calculate the cone angle.
+ cdp.theta_cone = order_parameters.theta_cone(s1)
# Monte Carlo simulation data structures.
if sim_index != None:
# Model parameters.
cdp.theta_axis_sim[sim_index] = theta_axis
cdp.phi_axis_sim[sim_index] = phi_axis
- cdp.theta_cone_sim[sim_index] = theta_cone
+ cdp.s1_sim[sim_index] = s1
# Normal data structures.
else:
# Model parameters.
cdp.theta_axis = theta_axis
cdp.phi_axis = phi_axis
- cdp.theta_cone = theta_cone
+ cdp.s1 = s1
# Wrap the Euler angles.
alpha = wrap_angles(alpha, 0.0, 2.0*pi)
@@ -637,7 +634,7 @@
- 'theta_axis', the cone axis polar angle (for the isotropic
cone model).
- 'phi_axis', the cone axis azimuthal angle (for the isotropic
cone model).
- - 'theta_cone', the isotropic cone angle.
+ - 's1', the isotropic cone order parameter.
@keyword set: The set of object names to return. This can
be set to 'all' for all
@@ -672,7 +669,7 @@
# Angular cone parameters.
names.append('theta_axis')
names.append('phi_axis')
- names.append('theta_cone')
+ names.append('s1')
# All other models.
else:
@@ -700,7 +697,7 @@
# Angular cone parameters.
names.append('theta_axis_err')
names.append('phi_axis_err')
- names.append('theta_cone_err')
+ names.append('s1_err')
# All other models.
else:
@@ -719,7 +716,7 @@
# Angular cone parameters.
names.append('theta_axis_sim')
names.append('phi_axis_sim')
- names.append('theta_cone_sim')
+ names.append('s1_sim')
# All other models.
else:
@@ -841,12 +838,12 @@
lower.append(0.0)
upper.append(2*pi * (1.0 - 1.0/incs[i]))
- # The cone angle.
- if cdp.params[i] == 'theta_cone':
+ # The cone order parameter.
+ if cdp.params[i] == 's1':
# Set the default bounds.
if default_bounds:
- lower.append(0.0)
- upper.append(pi)
+ lower.append(-0.5)
+ upper.append(1.0)
# Get the grid row.
if not row:
@@ -1048,9 +1045,9 @@
if search('phi[ -_]axis', param):
return 'phi_axis'
- # Cone angle.
- if search('theta[ -_]cone', param):
- return 'theta_cone'
+ # Cone order parameter.
+ if search('[Ss]1', param):
+ return 's1'
def return_error(self, spin_id):
r10612 - in /1.3: maths_fns/ specific_fns/