Author: bugman
Date: Tue Mar 5 11:33:43 2013
New Revision: 18631
URL: http://svn.gna.org/viewcvs/relax?rev=18631&view=rev
Log:
The frame order optimisation can now handle both types of pivot for the
average position rotation.
This allows the frame_order.average_position user function to be fully active.
Modified:
branches/frame_order_testing/maths_fns/frame_order/__init__.py
branches/frame_order_testing/specific_fns/frame_order.py
Modified: branches/frame_order_testing/maths_fns/frame_order/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/maths_fns/frame_order/__init__.py?rev=18631&r1=18630&r2=18631&view=diff
==============================================================================
--- branches/frame_order_testing/maths_fns/frame_order/__init__.py (original)
+++ branches/frame_order_testing/maths_fns/frame_order/__init__.py Tue Mar 5
11:33:43 2013
@@ -61,7 +61,7 @@
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, centroid=zeros(3),
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=zeros(3),
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.
@@ -100,8 +100,10 @@
@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 centroid: The central position to rotate all atoms
about. For example this can be the centre of mass of the moving domain.
- @type centroid: 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.
+ @type ave_pos_piv_sync: bool
@keyword translation_opt: A flag which if True will allow the
pivot point of the motion to be optimised.
@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.
@@ -135,7 +137,8 @@
self.paramag_centre = paramag_centre
self.total_num_params = len(init_params)
self.num_int_pts = num_int_pts
- self.centroid = centroid
+ self.ave_pos_pivot = ave_pos_pivot
+ self.ave_pos_piv_sync = ave_pos_piv_sync
self.translation_opt = translation_opt
self._param_pivot = pivot
self.pivot_opt = pivot_opt
@@ -1891,6 +1894,12 @@
@type RT_ave: numpy rank-2, 3D array
"""
+ # The rotational pivot.
+ if self.ave_pos_piv_sync:
+ ave_pos_pivot = self._param_pivot
+ else:
+ ave_pos_pivot = self.ave_pos_pivot
+
# The pivot to atom vectors.
for j in range(self.num_spins):
# The lanthanide to pivot vector.
@@ -1898,10 +1907,10 @@
self.r_ln_pivot[:, j] = pivot - self.paramag_centre
# Rotate then translate the atomic positions, then calculate the
pivot to atom vector.
- self.r_pivot_atom[:, j] = dot(R_ave, self.atomic_pos[j] -
self.centroid) + self.centroid
+ self.r_pivot_atom[:, j] = dot(R_ave, self.atomic_pos[j] -
ave_pos_pivot) + ave_pos_pivot
self.r_pivot_atom[:, j] += self._translation_vector
self.r_pivot_atom[:, j] -= pivot
- self.r_pivot_atom_rev[:, j] = dot(RT_ave, self.atomic_pos[j] -
self.centroid) + self.centroid
+ self.r_pivot_atom_rev[:, j] = dot(RT_ave, self.atomic_pos[j] -
ave_pos_pivot) + ave_pos_pivot
self.r_pivot_atom_rev[:, j] += self._translation_vector
self.r_pivot_atom_rev[:, j] -= pivot
Modified: branches/frame_order_testing/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/frame_order.py?rev=18631&r1=18630&r2=18631&view=diff
==============================================================================
--- branches/frame_order_testing/specific_fns/frame_order.py (original)
+++ branches/frame_order_testing/specific_fns/frame_order.py Tue Mar 5
11:33:43 2013
@@ -1372,6 +1372,10 @@
@type scaling: bool
"""
+ # Check for the average domain displacement information.
+ if not hasattr(cdp, 'ave_pos_pivot') or not hasattr(cdp,
'ave_pos_translation'):
+ raise RelaxError("The mechanics of the displacement to the
average domain position have not been set up.")
+
# Assemble the parameter vector.
param_vector = self._assemble_param_vector(sim_index=sim_index)
@@ -1408,9 +1412,6 @@
if 'pcs' in data_types or 'pre' in data_types:
atomic_pos, paramag_centre =
self._minimise_setup_atomic_pos(sim_index=sim_index)
- # The centre of mass of the moving domain - to use as the centroid
for the average domain position rotation.
- com = centre_of_mass(atom_id=self._domain_moving(), verbosity=0)
-
# Average domain translation.
translation_opt = False
if not self._translation_fixed():
@@ -1429,6 +1430,16 @@
# The number of integration points.
if not hasattr(cdp, 'num_int_pts'):
cdp.num_int_pts = 200000
+
+ # 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 = centre_of_mass(atom_id=self._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_piv_sync = True
# Print outs.
if sim_index == None:
@@ -1445,7 +1456,7 @@
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,
centroid=com, 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, 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
r18631 - in /branches/frame_order_testing: maths_fns/frame_order/__init__.py specific_fns/frame_order.py