Author: bugman
Date: Fri Nov 2 12:01:59 2012
New Revision: 17951
URL: http://svn.gna.org/viewcvs/relax?rev=17951&view=rev
Log:
Reverted r17950 as the vectors are dependent on the frame order eigenframe!
The command used was:
svn merge -r17950:17949 .
As the eigenframe changes during optimisation, the pre-calculation of Ln3+ to
atom vectors is not
possible.
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=17951&r1=17950&r2=17951&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 Fri Nov
2 12:01:59 2012
@@ -24,7 +24,7 @@
# Python module imports.
from math import cos, sin, sqrt
-from numpy import dot, float64, inner, transpose, zeros
+from numpy import dot, inner, transpose
from numpy.linalg import norm
# relax module imports.
@@ -187,11 +187,38 @@
@type error_flag: bool
"""
- # The vectors.
- rot_vect, rot_vect_rev, length, length_rev =
vectors_pivot_motion_full(theta_i=theta_i, phi_i=phi_i, sigma_i=sigma_i,
r_pivot_atom=r_pivot_atom, r_pivot_atom_rev=r_pivot_atom_rev,
r_ln_pivot=r_ln_pivot, R_eigen=R_eigen, RT_eigen=RT_eigen, Ri_prime=Ri_prime)
+ # The rotation matrix.
+ c_theta = cos(theta_i)
+ s_theta = sin(theta_i)
+ c_phi = cos(phi_i)
+ s_phi = sin(phi_i)
+ c_sigma_phi = cos(sigma_i - phi_i)
+ s_sigma_phi = sin(sigma_i - phi_i)
+ c_phi_c_theta = c_phi * c_theta
+ s_phi_c_theta = s_phi * c_theta
+ Ri_prime[0, 0] = c_phi_c_theta*c_sigma_phi - s_phi*s_sigma_phi
+ Ri_prime[0, 1] = -c_phi_c_theta*s_sigma_phi - s_phi*c_sigma_phi
+ Ri_prime[0, 2] = c_phi*s_theta
+ Ri_prime[1, 0] = s_phi_c_theta*c_sigma_phi + c_phi*s_sigma_phi
+ Ri_prime[1, 1] = -s_phi_c_theta*s_sigma_phi + c_phi*c_sigma_phi
+ Ri_prime[1, 2] = s_phi*s_theta
+ Ri_prime[2, 0] = -s_theta*c_sigma_phi
+ Ri_prime[2, 1] = s_theta*s_sigma_phi
+ Ri_prime[2, 2] = c_theta
+
+ # The rotation.
+ R_i = dot(R_eigen, dot(Ri_prime, RT_eigen))
+
+ # 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)
# 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
+
# Loop over the alignments.
for i in range(len(pcs_theta)):
# Skip missing data.
@@ -201,10 +228,10 @@
# The projection.
if full_in_ref_frame[i]:
proj = dot(rot_vect_rev[j], dot(A[i], rot_vect_rev[j]))
- length_i = length_rev[j]
+ length_i = length_rev
else:
proj = dot(rot_vect[j], dot(A[i], rot_vect[j]))
- length_i = length[j]
+ length_i = length
# The PCS.
pcs_theta[i, j] += proj * length_i
@@ -449,70 +476,5 @@
return matrix_rot
-def vectors_pivot_motion_full(theta_i=None, phi_i=None, sigma_i=None,
r_pivot_atom=None, r_pivot_atom_rev=None, r_ln_pivot=None, R_eigen=None,
RT_eigen=None, Ri_prime=None):
- """Calculate the lanthanide to atom vectors.
-
- @keyword theta_i: The half cone opening angle (polar angle).
- @type theta_i: float
- @keyword phi_i: The cone azimuthal angle.
- @type phi_i: float
- @keyword sigma_i: The torsion angle for state i.
- @type sigma_i: float
- @keyword r_pivot_atom: The pivot point to atom vector.
- @type r_pivot_atom: numpy rank-2, 3D array
- @keyword r_pivot_atom_rev: The reversed pivot point to atom vector.
- @type r_pivot_atom_rev: numpy rank-2, 3D array
- @keyword r_ln_pivot: The lanthanide position to pivot point
vector.
- @type r_ln_pivot: 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 empty rotation matrix for the in-frame
isotropic cone motion for state i.
- @type Ri_prime: numpy rank-2, 3D array
- @return: The vectors, reverse vectors, vector
lengths, and reverse vector lengths.
- @rtype: tuple of numpy rank-2, 3D array
- """
-
- # The rotation matrix.
- c_theta = cos(theta_i)
- s_theta = sin(theta_i)
- c_phi = cos(phi_i)
- s_phi = sin(phi_i)
- c_sigma_phi = cos(sigma_i - phi_i)
- s_sigma_phi = sin(sigma_i - phi_i)
- c_phi_c_theta = c_phi * c_theta
- s_phi_c_theta = s_phi * c_theta
- Ri_prime[0, 0] = c_phi_c_theta*c_sigma_phi - s_phi*s_sigma_phi
- Ri_prime[0, 1] = -c_phi_c_theta*s_sigma_phi - s_phi*c_sigma_phi
- Ri_prime[0, 2] = c_phi*s_theta
- Ri_prime[1, 0] = s_phi_c_theta*c_sigma_phi + c_phi*s_sigma_phi
- Ri_prime[1, 1] = -s_phi_c_theta*s_sigma_phi + c_phi*c_sigma_phi
- Ri_prime[1, 2] = s_phi*s_theta
- Ri_prime[2, 0] = -s_theta*c_sigma_phi
- Ri_prime[2, 1] = s_theta*s_sigma_phi
- Ri_prime[2, 2] = c_theta
-
- # The rotation.
- R_i = dot(R_eigen, dot(Ri_prime, RT_eigen))
-
- # 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)
-
- # Initialise the lengths.
- length = zeros(len(r_pivot_atom[0]), float64)
- length_rev = zeros(len(r_pivot_atom[0]), float64)
-
- # Loop over the atoms.
- for j in range(len(r_pivot_atom[0])):
- # The vector length (to the 5th power).
- length[j] = 1.0 / sqrt(inner(rot_vect[j], rot_vect[j]))**5
- length_rev[j] = 1.0 / sqrt(inner(rot_vect_rev[j],
rot_vect_rev[j]))**5
-
- # Return the data.
- return rot_vect, rot_vect_rev, length, length_rev
-
-
class Data:
"""A data container stored in the memo objects for use by the
Result_command class."""
r17951 - /branches/frame_order_testing/maths_fns/frame_order/matrix_ops.py