Author: bugman
Date: Fri Feb 14 17:54:31 2014
New Revision: 22194
URL: http://svn.gna.org/viewcvs/relax?rev=22194&view=rev
Log:
Implemented the new frame order rotor model parameters in the target function.
The parameters {axis_theta, axis_phi} have been replaced by the single
axis_alpha. To support the
new model construct, the CoM of the entire system is now passed into the
target function.
Modified:
branches/double_rotor/specific_analyses/frame_order/optimisation.py
branches/double_rotor/target_functions/frame_order.py
Modified: branches/double_rotor/specific_analyses/frame_order/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/double_rotor/specific_analyses/frame_order/optimisation.py?rev=22194&r1=22193&r2=22194&view=diff
==============================================================================
--- branches/double_rotor/specific_analyses/frame_order/optimisation.py
(original)
+++ branches/double_rotor/specific_analyses/frame_order/optimisation.py Fri
Feb 14 17:54:31 2014
@@ -683,14 +683,18 @@
if not hasattr(cdp, 'num_int_pts'):
cdp.num_int_pts = 200000
+ # The centre of mass, for use in the rotor models.
+ com = pipe_centre_of_mass(verbosity=0)
+ com = array(com, float64)
+
# The centre of mass of the moving domain - to use as the centroid for
the average domain position rotation.
if cdp.ave_pos_pivot == 'com':
- com = pipe_centre_of_mass(atom_id=domain_moving(), verbosity=0)
+ ave_pos_pivot = pipe_centre_of_mass(atom_id=domain_moving(),
verbosity=0)
ave_pos_piv_sync = False
# The centre of mass of the moving domain - to use as the centroid for
the average domain position rotation.
if cdp.ave_pos_pivot == 'motional':
- com = pivot
+ ave_pos_pivot = pivot
ave_pos_piv_sync = True
# Print outs.
@@ -709,7 +713,7 @@
sys.stdout.write("Base data: %s\n" % repr(base_data))
# Set up the optimisation function.
- target = frame_order.Frame_order(model=cdp.model,
init_params=param_vector, full_tensors=full_tensors,
full_in_ref_frame=full_in_ref_frame, rdcs=rdcs, rdc_errors=rdc_err,
rdc_weights=rdc_weight, rdc_vect=rdc_vect, dip_const=rdc_const, pcs=pcs,
pcs_errors=pcs_err, pcs_weights=pcs_weight, atomic_pos=atomic_pos, temp=temp,
frq=frq, paramag_centre=paramag_centre, scaling_matrix=scaling_matrix,
ave_pos_pivot=com, ave_pos_piv_sync=ave_pos_piv_sync,
translation_opt=translation_opt, pivot=pivot, pivot2=pivot2,
pivot_opt=pivot_opt, num_int_pts=cdp.num_int_pts, quad_int=cdp.quad_int)
+ target = frame_order.Frame_order(model=cdp.model,
init_params=param_vector, full_tensors=full_tensors,
full_in_ref_frame=full_in_ref_frame, rdcs=rdcs, rdc_errors=rdc_err,
rdc_weights=rdc_weight, rdc_vect=rdc_vect, dip_const=rdc_const, pcs=pcs,
pcs_errors=pcs_err, pcs_weights=pcs_weight, atomic_pos=atomic_pos, temp=temp,
frq=frq, paramag_centre=paramag_centre, scaling_matrix=scaling_matrix,
com=com, ave_pos_pivot=ave_pos_pivot, ave_pos_piv_sync=ave_pos_piv_sync,
translation_opt=translation_opt, pivot=pivot, pivot2=pivot2,
pivot_opt=pivot_opt, num_int_pts=cdp.num_int_pts, quad_int=cdp.quad_int)
# Return the data.
return target, param_vector, data_types, scaling_matrix
Modified: branches/double_rotor/target_functions/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/double_rotor/target_functions/frame_order.py?rev=22194&r1=22193&r2=22194&view=diff
==============================================================================
--- branches/double_rotor/target_functions/frame_order.py (original)
+++ branches/double_rotor/target_functions/frame_order.py Fri Feb 14 17:54:31
2014
@@ -25,7 +25,7 @@
# Python module imports.
from copy import deepcopy
from math import acos, pi, sqrt
-from numpy import array, dot, float32, float64, ones, transpose, uint8, zeros
+from numpy import array, cross, dot, float32, float64, ones, transpose,
uint8, zeros
from numpy.linalg import norm
# relax module imports.
@@ -46,7 +46,7 @@
from lib.frame_order.pseudo_ellipse_torsionless import
compile_2nd_matrix_pseudo_ellipse_torsionless,
pcs_numeric_int_pseudo_ellipse_torsionless,
pcs_numeric_int_pseudo_ellipse_torsionless_qrint
from lib.frame_order.rotor import compile_2nd_matrix_rotor,
pcs_numeric_int_rotor, pcs_numeric_int_rotor_qrint
from lib.geometry.coord_transform import spherical_to_cartesian
-from lib.geometry.rotations import euler_to_R_zyz, two_vect_to_R
+from lib.geometry.rotations import axis_angle_to_R, euler_to_R_zyz,
two_vect_to_R
from lib.linear_algebra.kronecker_product import kron_prod
from lib.order import order_parameters
from lib.physical_constants import pcs_constant
@@ -56,7 +56,7 @@
class Frame_order:
"""Class containing the target function of the optimisation of Frame
Order matrix components."""
- def __init__(self, model=None, init_params=None, full_tensors=None,
full_in_ref_frame=None, rdcs=None, rdc_errors=None, rdc_weights=None,
rdc_vect=None, dip_const=None, pcs=None, pcs_errors=None, pcs_weights=None,
atomic_pos=None, temp=None, frq=None, paramag_centre=zeros(3),
scaling_matrix=None, num_int_pts=500, ave_pos_pivot=zeros(3),
ave_pos_piv_sync=True, translation_opt=False, pivot=None, pivot2=None,
pivot_opt=False, quad_int=True):
+ def __init__(self, model=None, init_params=None, full_tensors=None,
full_in_ref_frame=None, rdcs=None, rdc_errors=None, rdc_weights=None,
rdc_vect=None, dip_const=None, pcs=None, pcs_errors=None, pcs_weights=None,
atomic_pos=None, temp=None, frq=None, paramag_centre=zeros(3),
scaling_matrix=None, num_int_pts=500, com=None, ave_pos_pivot=zeros(3),
ave_pos_piv_sync=True, translation_opt=False, pivot=None, pivot2=None,
pivot_opt=False, quad_int=True):
"""Set up the target functions for the Frame Order theories.
@keyword model: The name of the Frame Order model.
@@ -95,6 +95,8 @@
@type scaling_matrix: numpy rank-2 array
@keyword num_int_pts: The number of points to use for the
numerical integration technique.
@type num_int_pts: int
+ @keyword com: The centre of mass of the system. This
is used for defining the rotor model systems.
+ @type com: numpy 3D rank-1 array
@keyword ave_pos_pivot: The pivot point to rotate all atoms
about to the average domain position. For example this can be the centre of
mass of the moving domain.
@type ave_pos_pivot: numpy 3D rank-1 array
@keyword ave_pos_piv_sync: A flag which if True will cause pivot
point to rotate to the average domain position to be synchronised with the
motional pivot. This will cause ave_pos_pivot argument to be ignored.
@@ -134,6 +136,7 @@
self.paramag_centre = paramag_centre
self.total_num_params = len(init_params)
self.num_int_pts = num_int_pts
+ self.com = com
self.ave_pos_pivot = ave_pos_pivot
self.ave_pos_piv_sync = ave_pos_piv_sync
self.translation_opt = translation_opt
@@ -405,6 +408,9 @@
# Initialise the Frame Order matrices.
self.frame_order_2nd = zeros((9, 9), float64)
+ # A rotation matrix for general use.
+ self.R = zeros((3, 3), float64)
+
def func_double_rotor(self, params):
"""Target function for the optimisation of the double rotor frame
order model.
@@ -1879,18 +1885,23 @@
if self.translation_opt and self.pivot_opt:
self._param_pivot = params[:3]
self._translation_vector = params[3:6]
- ave_pos_alpha, ave_pos_beta, ave_pos_gamma, axis_theta,
axis_phi, sigma_max = params[6:]
+ ave_pos_alpha, ave_pos_beta, ave_pos_gamma, axis_alpha,
sigma_max = params[6:]
elif self.translation_opt:
self._translation_vector = params[:3]
- ave_pos_alpha, ave_pos_beta, ave_pos_gamma, axis_theta,
axis_phi, sigma_max = params[3:]
+ ave_pos_alpha, ave_pos_beta, ave_pos_gamma, axis_alpha,
sigma_max = params[3:]
elif self.pivot_opt:
self._param_pivot = params[:3]
- ave_pos_alpha, ave_pos_beta, ave_pos_gamma, axis_theta,
axis_phi, sigma_max = params[3:]
+ ave_pos_alpha, ave_pos_beta, ave_pos_gamma, axis_alpha,
sigma_max = params[3:]
else:
- ave_pos_alpha, ave_pos_beta, ave_pos_gamma, axis_theta,
axis_phi, sigma_max = params
-
- # Generate the cone axis from the spherical angles.
- spherical_to_cartesian([1.0, axis_theta, axis_phi], self.cone_axis)
+ ave_pos_alpha, ave_pos_beta, ave_pos_gamma, axis_alpha,
sigma_max = params
+
+ # Generate the rotation axis from the CoM, pivot point, and alpha
angle.
+ r_compiv = array(self._param_pivot, float64) - self.com
+ r_compiv = r_compiv / norm(r_compiv)
+ mu_xy = cross(r_compiv, self.z_axis)
+ mu_xy = mu_xy / norm(mu_xy)
+ axis_angle_to_R(r_compiv, axis_alpha, self.R)
+ self.cone_axis = dot(self.R, mu_xy)
# Pre-calculate the eigenframe rotation matrix.
two_vect_to_R(self.z_axis, self.cone_axis, self.R_eigen)
r22194 - in /branches/double_rotor: specific_analyses/frame_order/optimisation.py target_functions/frame_order.py