Author: bugman
Date: Tue Jun 17 11:30:47 2014
New Revision: 24017
URL: http://svn.gna.org/viewcvs/relax?rev=24017&view=rev
Log:
Speed up for the frame order analyses when only one domain is aligned.
When only one domain is aligned, the reverse Ln3+ to spin vectors for the PCS
are no longer
calculated. For most analyses, this should significantly reduce the number
of mathematical
operations required for the quasi-random Sobol' point numerical integration.
Modified:
branches/frame_order_cleanup/lib/frame_order/double_rotor.py
branches/frame_order_cleanup/lib/frame_order/matrix_ops.py
branches/frame_order_cleanup/lib/frame_order/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=24017&r1=24016&r2=24017&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/frame_order/double_rotor.py
(original)
+++ branches/frame_order_cleanup/lib/frame_order/double_rotor.py Tue
Jun 17 11:30:47 2014
@@ -176,13 +176,16 @@
@type missing_pcs: numpy rank-2 array
"""
- # Pre-calculate all the new vectors (forwards and reverse).
- rot_vect_rev = dot(r_pivot_atom_rev, Ri) + r_ln_pivot
+ # Pre-calculate all the new vectors.
rot_vect = dot(r_pivot_atom, Ri) + 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
+
+ # The reverse vectors and lengths.
+ if min(full_in_ref_frame) == 0:
+ rot_vect_rev = dot(r_pivot_atom_rev, Ri) + r_ln_pivot
+ length_rev = 1.0 / norm(rot_vect_rev, axis=1)**5
# Loop over the atoms.
for j in range(len(r_pivot_atom[:, 0])):
Modified: branches/frame_order_cleanup/lib/frame_order/matrix_ops.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/frame_order/matrix_ops.py?rev=24017&r1=24016&r2=24017&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/frame_order/matrix_ops.py (original)
+++ branches/frame_order_cleanup/lib/frame_order/matrix_ops.py Tue Jun 17
11:30:47 2014
@@ -111,13 +111,16 @@
@type missing_pcs: numpy rank-2 array
"""
- # Pre-calculate all the new vectors (forwards and reverse).
- rot_vect_rev = dot(r_pivot_atom_rev, Ri) + r_ln_pivot
+ # Pre-calculate all the new vectors.
rot_vect = dot(r_pivot_atom, Ri) + 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
+
+ # The reverse vectors and lengths.
+ if min(full_in_ref_frame) == 0:
+ rot_vect_rev = dot(r_pivot_atom_rev, Ri) + r_ln_pivot
+ length_rev = 1.0 / norm(rot_vect_rev, axis=1)**5
# Loop over the atoms.
for j in range(len(r_pivot_atom[:, 0])):
@@ -162,13 +165,16 @@
@type missing_pcs: numpy rank-2 array
"""
- # Pre-calculate all the new vectors (forwards and reverse).
- rot_vect_rev = dot(r_pivot_atom_rev, Ri) + r_ln_pivot
+ # Pre-calculate all the new vectors.
rot_vect = dot(r_pivot_atom, Ri) + 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
+
+ # The reverse vectors and lengths.
+ if min(full_in_ref_frame) == 0:
+ rot_vect_rev = dot(r_pivot_atom_rev, Ri) + r_ln_pivot
+ length_rev = 1.0 / norm(rot_vect_rev, axis=1)**5
# Loop over the atoms.
for j in range(len(r_pivot_atom[:, 0])):
Modified: branches/frame_order_cleanup/lib/frame_order/rotor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/frame_order/rotor.py?rev=24017&r1=24016&r2=24017&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/frame_order/rotor.py (original)
+++ branches/frame_order_cleanup/lib/frame_order/rotor.py Tue Jun 17
11:30:47 2014
@@ -176,13 +176,16 @@
@type missing_pcs: numpy rank-2 array
"""
- # Pre-calculate all the new vectors (forwards and reverse).
- rot_vect_rev = dot(r_pivot_atom_rev, Ri) + r_ln_pivot
+ # Pre-calculate all the new vectors.
rot_vect = dot(r_pivot_atom, Ri) + 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
+
+ # The reverse vectors and lengths.
+ if min(full_in_ref_frame) == 0:
+ rot_vect_rev = dot(r_pivot_atom_rev, Ri) + r_ln_pivot
+ length_rev = 1.0 / norm(rot_vect_rev, axis=1)**5
# Loop over the atoms.
for j in range(len(r_pivot_atom[:, 0])):
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=24017&r1=24016&r2=24017&view=diff
==============================================================================
--- branches/frame_order_cleanup/target_functions/frame_order.py
(original)
+++ branches/frame_order_cleanup/target_functions/frame_order.py Tue
Jun 17 11:30:47 2014
@@ -1159,10 +1159,11 @@
subtract(self.r_pivot_atom, pivot, self.r_pivot_atom)
# And the reverse vectors.
- self.r_pivot_atom_rev[:] = dot(vect, R_ave)
- 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)
+ if min(self.full_in_ref_frame) == 0:
+ self.r_pivot_atom_rev[:] = dot(vect, R_ave)
+ 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)
def create_sobol_data(self, n=10000, dims=None):
r24017 - in /branches/frame_order_cleanup: lib/frame_order/ target_functions/