Author: bugman
Date: Thu Dec 8 09:42:42 2011
New Revision: 15053
URL: http://svn.gna.org/viewcvs/relax?rev=15053&view=rev
Log:
Shifted the rotation to the average position to outside of the numerical
integration.
This now occurs once per function call, rather than hundreds of thousands of
times.
Modified:
branches/frame_order_testing/maths_fns/frame_order.py
branches/frame_order_testing/maths_fns/frame_order_matrix_ops.py
Modified: branches/frame_order_testing/maths_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/maths_fns/frame_order.py?rev=15053&r1=15052&r2=15053&view=diff
==============================================================================
--- branches/frame_order_testing/maths_fns/frame_order.py (original)
+++ branches/frame_order_testing/maths_fns/frame_order.py Thu Dec 8 09:42:42
2011
@@ -239,6 +239,7 @@
self.paramag_dist = zeros(self.num_pcs, float64)
self.pcs_const = zeros(self.num_align, float64)
self.r_pivot_atom = zeros((self.num_pcs, 3), float64)
+ self.r_pivot_atom_rev = zeros((self.num_pcs, 3), float64)
if self.paramag_centre == None:
self.paramag_centre = zeros(3, float64)
@@ -581,7 +582,7 @@
RT_ave = transpose(self.R_ave)
# Pre-calculate all the necessary vectors.
- self.calc_vectors(self._param_pivot)
+ self.calc_vectors(self._param_pivot, self.R_ave, RT_ave)
# Loop over each alignment.
for i in xrange(self.num_align):
@@ -604,12 +605,12 @@
if not self.missing_pcs[i, j]:
# Forwards and reverse rotations.
if self.full_in_ref_frame[i]:
- R_ave = RT_ave
+ r_pivot_atom = self.r_pivot_atom_rev[j]
else:
- R_ave = self.R_ave
+ r_pivot_atom = self.r_pivot_atom[j]
# The numerical integration.
- self.pcs_theta[i, j] =
pcs_numeric_int_rotor(sigma_max=sigma_max, c=self.pcs_const[i],
r_pivot_atom=self.r_pivot_atom[j], r_ln_pivot=self.r_ln_pivot,
A=self.A_3D[i], R_ave=R_ave, R_eigen=self.R_eigen, RT_eigen=RT_eigen,
Ri_prime=self.Ri_prime)
+ self.pcs_theta[i, j] =
pcs_numeric_int_rotor(sigma_max=sigma_max, c=self.pcs_const[i],
r_pivot_atom=r_pivot_atom, r_ln_pivot=self.r_ln_pivot, A=self.A_3D[i],
R_eigen=self.R_eigen, RT_eigen=RT_eigen, Ri_prime=self.Ri_prime)
# Calculate and sum the single alignment chi-squared value
(for the PCS).
chi2_sum = chi2_sum + chi2(self.pcs[i], self.pcs_theta[i],
self.pcs_error[i])
@@ -618,11 +619,15 @@
return chi2_sum
- def calc_vectors(self, pivot):
+ def calc_vectors(self, pivot, R_ave, RT_ave):
"""Calculate the pivot to atom and lanthanide to pivot vectors for
the target functions.
@param pivot: The pivot point.
@type pivot: numpy rank-1, 3D array
+ @param R_ave: The rotation matrix for rotating from the reference
frame to the average position.
+ @type R_ave: numpy rank-2, 3D array
+ @param RT_ave: The transpose of R_ave.
+ @type RT_ave: numpy rank-2, 3D array
"""
# The lanthanide to pivot vector.
@@ -630,8 +635,9 @@
# The pivot to atom vectors.
for j in xrange(self.num_pcs):
- # The vector.
- self.r_pivot_atom[j] = self.pcs_atoms[j] - pivot
+ # The rotated vectors.
+ self.r_pivot_atom[j] = dot(R_ave, self.pcs_atoms[j] - pivot)
+ self.r_pivot_atom_rev[j] = dot(RT_ave, self.pcs_atoms[j] - pivot)
def reduce_and_rot(self, ave_pos_alpha=None, ave_pos_beta=None,
ave_pos_gamma=None, daeg=None):
Modified: branches/frame_order_testing/maths_fns/frame_order_matrix_ops.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/maths_fns/frame_order_matrix_ops.py?rev=15053&r1=15052&r2=15053&view=diff
==============================================================================
--- branches/frame_order_testing/maths_fns/frame_order_matrix_ops.py
(original)
+++ branches/frame_order_testing/maths_fns/frame_order_matrix_ops.py Thu Dec
8 09:42:42 2011
@@ -1298,7 +1298,7 @@
return 2 - 2*cos(tmax)**3
-def pcs_numeric_int_rotor(sigma_max=None, c=None, r_pivot_atom=None,
r_ln_pivot=None, A=None, R_ave=None, R_eigen=None, RT_eigen=None,
Ri_prime=None):
+def pcs_numeric_int_rotor(sigma_max=None, c=None, r_pivot_atom=None,
r_ln_pivot=None, A=None, R_eigen=None, RT_eigen=None, Ri_prime=None):
"""Determine the averaged PCS value via numerical integration.
@keyword sigma_max: The maximum rotor angle.
@@ -1311,8 +1311,6 @@
@type r_ln_pivot: numpy rank-1, 3D array
@keyword A: The full alignment tensor of the non-moving
domain.
@type A: numpy rank-2, 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 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).
@@ -1330,11 +1328,8 @@
Ri_prime[2, 1] = 0.0
Ri_prime[2, 2] = 1.0
- # Pre-calculate a dot product for speed ups in the integration.
- dot_RT_eigen_R_ave = dot(RT_eigen, R_ave)
-
# Perform numerical integration.
- result = quad(pcs_pivot_motion_rotor, -sigma_max, sigma_max, args=(c,
r_pivot_atom, r_ln_pivot, A, R_ave, R_eigen, RT_eigen, Ri_prime,
dot_RT_eigen_R_ave))
+ result = quad(pcs_pivot_motion_rotor, -sigma_max, sigma_max, args=(c,
r_pivot_atom, r_ln_pivot, A, R_eigen, RT_eigen, Ri_prime))
# The surface area normalisation factor.
SA = 2.0 * sigma_max
@@ -1343,7 +1338,7 @@
return result[0] / SA
-def pcs_pivot_motion_rotor(sigma_i, c, r_pivot_atom, r_ln_pivot, A, R_ave,
R_eigen, RT_eigen, Ri_prime, dot_RT_eigen_R_ave):
+def pcs_pivot_motion_rotor(sigma_i, c, r_pivot_atom, r_ln_pivot, A, R_eigen,
RT_eigen, Ri_prime):
"""Calculate the PCS value after a pivoted motion for the rotor model.
@param sigma_i: The rotor angle for state i.
@@ -1356,16 +1351,12 @@
@type r_ln_pivot: numpy rank-1, 3D array
@param A: The full alignment tensor of the non-moving
domain.
@type A: numpy rank-2, 3D array
- @param R_ave: The rotation matrix for rotating from the
reference frame to the average position.
- @type R_ave: numpy rank-2, 3D array
@param R_eigen: The eigenframe rotation matrix.
@type R_eigen: numpy rank-2, 3D array
@param RT_eigen: The transpose of the eigenframe rotation
matrix (for faster calculations).
@type RT_eigen: numpy rank-2, 3D array
@param Ri_prime: The empty rotation matrix for the in-frame
rotor motion for state i.
@type Ri_prime: numpy rank-2, 3D array
- @param dot_RT_eigen_R_ave: The dot product of RT_eigen and R_ave to
speed up this calculation.
- @type dot_RT_eigen_R_ave: numpy rank-2, 3D array
@return: The PCS value for the changed position.
@rtype: float
"""
@@ -1379,7 +1370,7 @@
Ri_prime[1, 1] = c_sigma
# The rotation.
- R_i = dot(R_eigen, dot(Ri_prime, dot_RT_eigen_R_ave))
+ R_i = dot(R_eigen, dot(Ri_prime, RT_eigen))
# Calculate the new vector.
vect = dot(R_i, r_pivot_atom) + r_ln_pivot
r15053 - in /branches/frame_order_testing/maths_fns: frame_order.py frame_order_matrix_ops.py