r23389 - /trunk/lib/frame_order/matrix_ops.py -- May 23, 2014 - 19:39

Author: bugman
Date: Fri May 23 19:39:53 2014
New Revision: 23389

URL: http://svn.gna.org/viewcvs/relax?rev=23389&view=rev
Log:
Small speed up for all the isotropic cone and pseudo-elliptic cone frame 
order models.

The vector length calculation for the numeric PCS integration has been 
simplified and shifted
outside of a loop to take advantage of the speed of numpy.


Modified:
    trunk/lib/frame_order/matrix_ops.py

Modified: trunk/lib/frame_order/matrix_ops.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/matrix_ops.py?rev=23389&r1=23388&r2=23389&view=diff
==============================================================================
--- trunk/lib/frame_order/matrix_ops.py (original)
+++ trunk/lib/frame_order/matrix_ops.py Fri May 23 19:39:53 2014
@@ -23,8 +23,8 @@
 """Module for the handling of Frame Order."""
 
 # Python module imports.
-from math import cos, sin, sqrt
-from numpy import dot, inner, transpose
+from math import cos, sin
+from numpy import dot, inner, sqrt, transpose
 from numpy.linalg import norm
 
 # relax module imports.
@@ -198,12 +198,12 @@
     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)
 
+    # 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
+
     # 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.
@@ -213,10 +213,10 @@
             # The projection.
             if full_in_ref_frame[i]:
                 proj = dot(rot_vect[j], dot(A[i], rot_vect[j]))
-                length_i = length
+                length_i = length[j]
             else:
                 proj = dot(rot_vect_rev[j], dot(A[i], rot_vect_rev[j]))
-                length_i = length_rev
+                length_i = length_rev[j]
 
             # The PCS.
             pcs_theta[i, j] += proj * length_i
@@ -342,12 +342,12 @@
     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)
 
+    # 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
+
     # 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.
@@ -357,10 +357,10 @@
             # The projection.
             if full_in_ref_frame[i]:
                 proj = dot(rot_vect[j], dot(A[i], rot_vect[j]))
-                length_i = length
+                length_i = length[j]
             else:
                 proj = dot(rot_vect_rev[j], dot(A[i], rot_vect_rev[j]))
-                length_i = length_rev
+                length_i = length_rev[j]
 
             # The PCS.
             pcs_theta[i, j] += proj * length_i