Author: bugman
Date: Mon Jun 16 11:49:10 2014
New Revision: 23974
URL: http://svn.gna.org/viewcvs/relax?rev=23974&view=rev
Log:
Updated the double rotor frame order model to be in a pseudo-functional state.
Bugs in the target function method have been removed, the calc_vectors()
target function now accepts
the pivot2 argument (but does nothing with it yet), and the
lib.frame_order.double_rotor module has
been updated to match the logic used in all other lib.frame_order modules.
Modified:
branches/frame_order_cleanup/lib/frame_order/double_rotor.py
branches/frame_order_cleanup/target_functions/frame_order.py
Modified: branches/frame_order_cleanup/lib/frame_order/double_rotor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/frame_order/double_rotor.py?rev=23974&r1=23973&r2=23974&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/frame_order/double_rotor.py
(original)
+++ branches/frame_order_cleanup/lib/frame_order/double_rotor.py Mon
Jun 16 11:49:10 2014
@@ -24,7 +24,8 @@
# Python module imports.
from math import pi, sqrt
-from numpy import divide, dot, inner, multiply, sinc, transpose
+from numpy import divide, dot, inner, multiply, sinc, swapaxes, tensordot,
transpose
+from numpy.linalg import norm
# relax module imports.
from lib.frame_order.matrix_ops import rotate_daeg
@@ -147,7 +148,7 @@
divide(pcs_theta, float(num), pcs_theta)
-def pcs_pivot_motion_double_rotor(full_in_ref_frame=None, r_pivot_atom=None,
r_pivot_atom_rev=None, r_ln_pivot=None, A=None, R_eigen=None, RT_eigen=None,
Ri_prime=None, pcs_theta=None, pcs_theta_err=None, missing_pcs=None):
+def pcs_pivot_motion_double_rotor(full_in_ref_frame=None, r_pivot_atom=None,
r_pivot_atom_rev=None, r_ln_pivot=None, A=None, Ri=None, pcs_theta=None,
pcs_theta_err=None, missing_pcs=None):
"""Calculate the PCS value after a pivoted motion for the double rotor
model.
@keyword full_in_ref_frame: An array of flags specifying if the tensor
in the reference frame is the full or reduced tensor.
@@ -160,12 +161,8 @@
@type r_ln_pivot: numpy rank-2, 3D array
@keyword A: The full alignment tensor of the non-moving
domain.
@type A: numpy rank-2, 3D array
- @keyword R_eigen: The eigenframe rotation matrix.
- @type R_eigen: numpy rank-2, 3D array
- @keyword RT_eigen: The transpose of the eigenframe rotation
matrix (for faster calculations).
- @type RT_eigen: numpy rank-2, 3D array
- @keyword Ri_prime: The pre-calculated rotation matrix for the
in-frame double rotor motion for state i.
- @type Ri_prime: numpy rank-2, 3D array
+ @keyword Ri: The frame-shifted, pre-calculated rotation
matrix for state i.
+ @type Ri: numpy rank-2, 3D array
@keyword pcs_theta: The storage structure for the
back-calculated PCS values.
@type pcs_theta: numpy rank-2 array
@keyword pcs_theta_err: The storage structure for the
back-calculated PCS errors.
@@ -174,19 +171,16 @@
@type missing_pcs: numpy rank-2 array
"""
- # The rotation.
- R_i = dot(R_eigen, dot(Ri_prime, RT_eigen))
+ # Pre-calculate all the new vectors (forwards and reverse).
+ rot_vect_rev = dot(r_pivot_atom_rev, Ri) + r_ln_pivot
+ rot_vect = dot(r_pivot_atom, Ri) + r_ln_pivot
- # Pre-calculate all the new vectors (forwards and reverse).
- rot_vect_rev = transpose(dot(R_i, r_pivot_atom_rev) + r_ln_pivot)
- rot_vect = transpose(dot(R_i, r_pivot_atom) + r_ln_pivot)
+ # The vector length (to the 5th power).
+ length_rev = 1.0 / norm(rot_vect_rev, axis=1)**5
+ length = 1.0 / norm(rot_vect, axis=1)**5
# Loop over the atoms.
- for j in range(len(r_pivot_atom[0])):
- # The vector length (to the 5th power).
- length_rev = 1.0 / sqrt(inner(rot_vect_rev[j], rot_vect_rev[j]))**5
- length = 1.0 / sqrt(inner(rot_vect[j], rot_vect[j]))**5
-
+ for j in range(len(r_pivot_atom[:, 0])):
# Loop over the alignments.
for i in range(len(pcs_theta)):
# Skip missing data.
@@ -196,10 +190,10 @@
# The projection.
if full_in_ref_frame[i]:
proj = dot(rot_vect[j], dot(A[i], rot_vect[j]))
- length_i = length
+ length_i = length[j]
else:
proj = dot(rot_vect_rev[j], dot(A[i], rot_vect_rev[j]))
- length_i = length_rev
+ length_i = length_rev[j]
# The PCS.
pcs_theta[i, j] += proj * length_i
Modified: branches/frame_order_cleanup/target_functions/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/target_functions/frame_order.py?rev=23974&r1=23973&r2=23974&view=diff
==============================================================================
--- branches/frame_order_cleanup/target_functions/frame_order.py
(original)
+++ branches/frame_order_cleanup/target_functions/frame_order.py Mon
Jun 16 11:49:10 2014
@@ -431,7 +431,7 @@
# PCS via numerical integration.
if self.pcs_flag:
# Numerical integration of the PCSs.
- pcs_numeric_int_double_rotor(points=self.sobol_angles,
sigma_max=sigma_max, sigma_max_2=sigma_max_2, c=self.pcs_const,
full_in_ref_frame=self.full_in_ref_frame, r_pivot_atom=self.r_pivot_atom,
r_pivot_atom_rev=self.r_pivot_atom_rev, r_ln_pivot=self.r_ln_pivot,
A=self.A_3D, R_eigen=R_eigen_full, RT_eigen=RT_eigen, Ri_prime=self.Ri_prime,
pcs_theta=self.pcs_theta, pcs_theta_err=self.pcs_theta_err,
missing_pcs=self.missing_pcs)
+ pcs_numeric_int_double_rotor(points=self.sobol_angles,
sigma_max=sigma_max, sigma_max_2=sigma_max_2, c=self.pcs_const,
full_in_ref_frame=self.full_in_ref_frame, r_pivot_atom=self.r_pivot_atom,
r_pivot_atom_rev=self.r_pivot_atom_rev, r_ln_pivot=self.r_ln_pivot,
A=self.A_3D, R_eigen=self.R_eigen, RT_eigen=RT_eigen, Ri_prime=self.Ri_prime,
pcs_theta=self.pcs_theta, pcs_theta_err=self.pcs_theta_err,
missing_pcs=self.missing_pcs)
# Calculate and sum the single alignment chi-squared value (for
the PCS).
for align_index in range(self.num_align):
@@ -1132,11 +1132,13 @@
return chi2_sum
- def calc_vectors(self, pivot=None, R_ave=None, RT_ave=None):
+ def calc_vectors(self, pivot=None, pivot2=None, R_ave=None, RT_ave=None):
"""Calculate the pivot to atom and lanthanide to pivot vectors for
the target functions.
@keyword pivot: The pivot point.
@type pivot: numpy rank-1, 3D array
+ @keyword pivot2: The 2nd pivot point.
+ @type pivot2: numpy rank-1, 3D array
@keyword R_ave: The rotation matrix for rotating from the
reference frame to the average position.
@type R_ave: numpy rank-2, 3D array
@keyword RT_ave: The transpose of R_ave.
r23974 - in /branches/frame_order_cleanup: lib/frame_order/double_rotor.py target_functions/frame_order.py