Author: bugman
Date: Wed Dec 7 10:47:48 2011
New Revision: 15039
URL: http://svn.gna.org/viewcvs/relax?rev=15039&view=rev
Log:
Pre-calculation of a dot product to speed up numerical integration of the
rotor frame order PCS.
Modified:
branches/frame_order_testing/maths_fns/frame_order_matrix_ops.py
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=15039&r1=15038&r2=15039&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 Wed Dec
7 10:47:48 2011
@@ -1330,8 +1330,11 @@
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),
full_output=1)
+ 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), full_output=1)
# The surface area normalisation factor.
SA = 2.0 * sigma_max
@@ -1340,29 +1343,31 @@
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):
+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):
"""Calculate the PCS value after a pivoted motion for the rotor model.
- @param sigma_i: The rotor angle for state i.
- @type sigma_i: float
- @param c: The PCS constant (without the interatomic
distance and in Angstrom units).
- @type c: float
- @param r_pivot_atom: The pivot point to atom vector.
- @type r_pivot_atom: numpy rank-1, 3D array
- @param r_ln_pivot: The lanthanide position to pivot point vector.
- @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
- @return: The PCS value for the changed position.
- @rtype: float
+ @param sigma_i: The rotor angle for state i.
+ @type sigma_i: float
+ @param c: The PCS constant (without the interatomic
distance and in Angstrom units).
+ @type c: float
+ @param r_pivot_atom: The pivot point to atom vector.
+ @type r_pivot_atom: numpy rank-1, 3D array
+ @param r_ln_pivot: The lanthanide position to pivot point
vector.
+ @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
"""
# The rotation matrix.
@@ -1374,8 +1379,7 @@
Ri_prime[1, 1] = c_sigma
# The rotation.
- #RT_i = dot(R_ave, dot(R_eigen, dot(transpose(Ri_prime), RT_eigen)))
- R_i = dot(R_eigen, dot(Ri_prime, dot(RT_eigen, R_ave)))
+ R_i = dot(R_eigen, dot(Ri_prime, dot_RT_eigen_R_ave))
# Calculate the new vector.
vect = dot(R_i, r_pivot_atom) + r_ln_pivot
r15039 - /branches/frame_order_testing/maths_fns/frame_order_matrix_ops.py