Author: bugman
Date: Wed Jun 18 15:38:33 2014
New Revision: 24090
URL: http://svn.gna.org/viewcvs/relax?rev=24090&view=rev
Log:
Support for the 3 vector system for double motions has been added to the
frame order analysis.
This is used for the quasi-random Sobol' numeric integration of the PCS. The
lanthanide to atom
vector is the sum of three parts: the 1st pivot to atom vector rotated by
the 1st mode of motion;
the 2nd pivot to 1st pivot vector rotated by the 2nd mode of motion (together
with the rotated 1st
pivot to atom vectors); and the lanthanide to second pivot vector.
All these vectors are passed into the
lib.frame_order.double_rotor.pcs_numeric_int_double_rotor()
function, which passes them to the pcs_pivot_motion_double_rotor() function
where they are rotated
and reconstructed into the Ln3+ to atom vectors.
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=24090&r1=24089&r2=24090&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/frame_order/double_rotor.py
(original)
+++ branches/frame_order_cleanup/lib/frame_order/double_rotor.py Wed
Jun 18 15:38:33 2014
@@ -24,7 +24,7 @@
# Python module imports.
from math import pi, sqrt
-from numpy import divide, dot, inner, multiply, sinc, swapaxes, tensordot,
transpose
+from numpy import add, divide, dot, inner, multiply, sinc, swapaxes,
tensordot, transpose
from numpy.linalg import norm
# relax module imports.
@@ -75,7 +75,7 @@
return rotate_daeg(matrix, Rx2_eigen)
-def pcs_numeric_int_double_rotor(points=None, sigma_max=None,
sigma_max_2=None, c=None, 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_numeric_int_double_rotor(points=None, sigma_max=None,
sigma_max_2=None, c=None, full_in_ref_frame=None, r_pivot_atom=None,
r_pivot_atom_rev=None, r_ln_pivot=None, r_inter_pivot=None, A=None,
R_eigen=None, RT_eigen=None, Ri_prime=None, pcs_theta=None,
pcs_theta_err=None, missing_pcs=None):
"""The averaged PCS value via numerical integration for the double rotor
frame order model.
@keyword points: The Sobol points in the torsion-tilt angle
space.
@@ -94,6 +94,8 @@
@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_inter_pivot: The vector between the two pivots.
+ @type r_inter_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_eigen: The eigenframe rotation matrix.
@@ -129,7 +131,7 @@
continue
# Calculate the PCSs for this state.
- pcs_pivot_motion_double_rotor(full_in_ref_frame=full_in_ref_frame,
r_pivot_atom=r_pivot_atom, r_pivot_atom_rev=r_pivot_atom_rev,
r_ln_pivot=r_ln_pivot, A=A, Ri=Ri[i], pcs_theta=pcs_theta,
pcs_theta_err=pcs_theta_err, missing_pcs=missing_pcs)
+ pcs_pivot_motion_double_rotor(full_in_ref_frame=full_in_ref_frame,
r_pivot_atom=r_pivot_atom, r_pivot_atom_rev=r_pivot_atom_rev,
r_ln_pivot=r_ln_pivot, r_inter_pivot=r_inter_pivot, A=A, Ri=Ri[i], Ri2=Ri[i],
pcs_theta=pcs_theta, pcs_theta_err=pcs_theta_err, missing_pcs=missing_pcs)
# Increment the number of points.
num += 1
@@ -142,7 +144,7 @@
Ri = swapaxes(Ri, 0, 1)
# Calculate the PCSs for this state.
- pcs_pivot_motion_double_rotor(full_in_ref_frame=full_in_ref_frame,
r_pivot_atom=r_pivot_atom, r_pivot_atom_rev=r_pivot_atom_rev,
r_ln_pivot=r_ln_pivot, A=A, Ri=Ri, pcs_theta=pcs_theta,
pcs_theta_err=pcs_theta_err, missing_pcs=missing_pcs)
+ pcs_pivot_motion_double_rotor(full_in_ref_frame=full_in_ref_frame,
r_pivot_atom=r_pivot_atom, r_pivot_atom_rev=r_pivot_atom_rev,
r_ln_pivot=r_ln_pivot, r_inter_pivot=r_inter_pivot, A=A, Ri=Ri, Ri2=Ri,
pcs_theta=pcs_theta, pcs_theta_err=pcs_theta_err, missing_pcs=missing_pcs)
# Multiply the constant.
multiply(c, pcs_theta, pcs_theta)
@@ -153,7 +155,7 @@
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, Ri=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, r_inter_pivot=None, A=None, Ri=None,
Ri2=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.
@@ -164,10 +166,14 @@
@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_inter_pivot: The vector between the two pivots.
+ @type r_inter_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 Ri: The frame-shifted, pre-calculated rotation
matrix for state i.
+ @keyword Ri: The frame-shifted, pre-calculated rotation
matrix for state i for the first mode of motion.
@type Ri: numpy rank-2, 3D array
+ @keyword Ri2: The frame-shifted, pre-calculated rotation
matrix for state i for the second mode of motion.
+ @type Ri2: 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.
@@ -176,15 +182,27 @@
@type missing_pcs: numpy rank-2 array
"""
- # Pre-calculate all the new vectors.
+ # Rotate the first pivot to atomic position vectors.
rot_vect = dot(r_pivot_atom, Ri) + r_ln_pivot
+
+ # Add the inter-pivot vector to obtain the 2nd pivot to atomic position
vectors.
+ add(r_inter_pivot, rot_vect, rot_vect)
+
+ # Rotate the 2nd pivot to atomic position vectors.
+ rot_vect = dot(rot_vect, Ri2)
+
+ # Add the lanthanide to pivot vector.
+ add(rot_vect, r_ln_pivot, rot_vect)
# The vector length (to the 5th power).
length = 1.0 / norm(rot_vect, axis=1)**5
# The reverse vectors and lengths.
if min(full_in_ref_frame) == 0:
- rot_vect_rev = dot(r_pivot_atom_rev, Ri) + r_ln_pivot
+ rot_vect_rev = dot(r_pivot_atom_rev, Ri)
+ add(r_inter_pivot, rot_vect_rev, rot_vect_rev)
+ rot_vect_rev = dot(rot_vect_rev, Ri2)
+ add(rot_vect_rev, r_ln_pivot, rot_vect_rev)
length_rev = 1.0 / norm(rot_vect_rev, axis=1)**5
# Loop over the atoms.
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=24090&r1=24089&r2=24090&view=diff
==============================================================================
--- branches/frame_order_cleanup/target_functions/frame_order.py
(original)
+++ branches/frame_order_cleanup/target_functions/frame_order.py Wed
Jun 18 15:38:33 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=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)
+ 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,
r_inter_pivot=self.r_inter_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):
@@ -1164,6 +1164,10 @@
add(self.r_pivot_atom_rev, self.ave_pos_pivot,
self.r_pivot_atom_rev)
add(self.r_pivot_atom_rev, self._translation_vector,
self.r_pivot_atom_rev)
subtract(self.r_pivot_atom_rev, pivot, self.r_pivot_atom_rev)
+
+ # Calculate the inter-pivot vector for the double motion models.
+ if pivot2 != None:
+ self.r_inter_pivot = pivot - pivot2
def create_sobol_data(self, n=10000, dims=None):
r24090 - in /branches/frame_order_cleanup: lib/frame_order/double_rotor.py target_functions/frame_order.py