Author: bugman
Date: Wed Feb 12 16:20:38 2014
New Revision: 22177
URL: http://svn.gna.org/viewcvs/relax?rev=22177&view=rev
Log:
The second pivot is now being passed into the frame order target function
class.
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=22177&r1=22176&r2=22177&view=diff
==============================================================================
--- branches/double_rotor/specific_analyses/frame_order/optimisation.py
(original)
+++ branches/double_rotor/specific_analyses/frame_order/optimisation.py Wed
Feb 12 16:20:38 2014
@@ -669,6 +669,11 @@
if hasattr(cdp, 'pivot'):
pivot = cdp.pivot
+ # The second pivot.
+ pivot2 = None
+ if hasattr(cdp, 'pivot2'):
+ pivot2 = cdp.pivot2
+
# Pivot optimisation.
pivot_opt = True
if pivot_fixed():
@@ -704,7 +709,7 @@
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, 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,
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)
# 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=22177&r1=22176&r2=22177&view=diff
==============================================================================
--- branches/double_rotor/target_functions/frame_order.py (original)
+++ branches/double_rotor/target_functions/frame_order.py Wed Feb 12 16:20:38
2014
@@ -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=zeros(3),
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, 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.
@@ -103,6 +103,8 @@
@type translation_opt: bool
@keyword pivot: The pivot point for the ball-and-socket
joint motion. This is needed if PCS or PRE values are used.
@type pivot: numpy rank-1, 3D array or None
+ @keyword pivot2: The second pivot point for the motion.
This is needed if PCS or PRE values are used and if a double-motional model
is to be optimised.
+ @type pivot2: numpy rank-1, 3D array or None
@keyword pivot_opt: A flag which if True will allow the
pivot point of the motion to be optimised.
@type pivot_opt: bool
@keyword quad_int: A flag which if True will perform high
precision numerical integration via the scipy.integrate quad(), dblquad() and
tplquad() integration methods rather than the rough quasi-random numerical
integration.
@@ -136,6 +138,7 @@
self.ave_pos_piv_sync = ave_pos_piv_sync
self.translation_opt = translation_opt
self._param_pivot = pivot
+ self._param_pivot2 = pivot2
self.pivot_opt = pivot_opt
# Tensor setup.
@@ -422,7 +425,7 @@
# Unpack the parameters.
if self.translation_opt and self.pivot_opt:
self._param_pivot = params[:3]
- self._param_pivot_2 = params[3:6]
+ self._param_pivot2 = params[3:6]
self._translation_vector = params[6:9]
ave_pos_alpha, ave_pos_beta, ave_pos_gamma, axis_theta,
axis_phi, axis_theta_2, axis_phi_2, sigma_max, sigma_max_2 = params[9:]
elif self.translation_opt:
@@ -430,7 +433,7 @@
ave_pos_alpha, ave_pos_beta, ave_pos_gamma, axis_theta,
axis_phi, axis_theta_2, axis_phi_2, sigma_max, sigma_max_2 = params[3:]
elif self.pivot_opt:
self._param_pivot = params[:3]
- self._param_pivot_2 = params[3:6]
+ self._param_pivot2 = params[3:6]
ave_pos_alpha, ave_pos_beta, ave_pos_gamma, axis_theta,
axis_phi, axis_theta_2, axis_phi_2, sigma_max, sigma_max_2 = params[6:]
else:
ave_pos_alpha, ave_pos_beta, ave_pos_gamma, axis_theta,
axis_phi, axis_theta_2, axis_phi_2, sigma_max, sigma_max_2 = params
r22177 - in /branches/double_rotor: specific_analyses/frame_order/optimisation.py target_functions/frame_order.py