Author: bugman
Date: Fri Jun 13 19:51:26 2014
New Revision: 23947
URL: http://svn.gna.org/viewcvs/relax?rev=23947&view=rev
Log:
Added another timing script for helping with speeding up the frame order
analysis.
This is for the part where the rotation matrix for each Sobol' integration
point is shifted into the
eigenframe.
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/timings/frame_rotations.log
branches/frame_order_cleanup/test_suite/shared_data/frame_order/timings/frame_rotations.py
- copied, changed from r23936,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/timings/tensor_projections.py
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/timings/frame_rotations.log
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/timings/frame_rotations.log?rev=23947&view=auto
==============================================================================
---
branches/frame_order_cleanup/test_suite/shared_data/frame_order/timings/frame_rotations.log
(added)
+++
branches/frame_order_cleanup/test_suite/shared_data/frame_order/timings/frame_rotations.log
Fri Jun 13 19:51:26 2014
@@ -0,0 +1,37 @@
+Original matrices:
+[[[ 1. 2. 3.]
+ [ 2. 3. 4.]
+ [ 3. 4. 5.]]
+
+ [[ 1. 2. 3.]
+ [ 2. 3. 4.]
+ [ 3. 4. 5.]]]
+Shape: (100, 3, 3)
+
+R:
+[[-0.147233 -0.65802651 0.73846026]
+ [ 0.87841732 0.25618968 0.40342268]
+ [-0.45464871 0.70807342 0.54030231]]
+
+
+1st rotation - element by element R.Ri[i].RT.
+Rotations:
+[[[-0.10494087 1.08573414 0.47747559]
+ [ 1.08573414 5.63549417 4.81557522]
+ [ 0.47747559 4.81557522 3.4694467 ]]
+
+ [[-0.10494087 1.08573414 0.47747559]
+ [ 1.08573414 5.63549417 4.81557522]
+ [ 0.47747559 4.81557522 3.4694467 ]]]
+Timing (s): 24.9873549938
+
+2nd rotation - dot of tensordot, and axis swap.
+Rotations:
+[[[-0.10494087 1.08573414 0.47747559]
+ [ 1.08573414 5.63549417 4.81557522]
+ [ 0.47747559 4.81557522 3.4694467 ]]
+
+ [[-0.10494087 1.08573414 0.47747559]
+ [ 1.08573414 5.63549417 4.81557522]
+ [ 0.47747559 4.81557522 3.4694467 ]]]
+Timing (s): 3.01101016998
Copied:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/timings/frame_rotations.py
(from r23936,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/timings/tensor_projections.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/timings/frame_rotations.py?p2=branches/frame_order_cleanup/test_suite/shared_data/frame_order/timings/frame_rotations.py&p1=branches/frame_order_cleanup/test_suite/shared_data/frame_order/timings/tensor_projections.py&r1=23936&r2=23947&rev=23947&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/shared_data/frame_order/timings/tensor_projections.py
(original)
+++
branches/frame_order_cleanup/test_suite/shared_data/frame_order/timings/frame_rotations.py
Fri Jun 13 19:51:26 2014
@@ -1,9 +1,7 @@
# Python module imports.
from numpy import *
-from numpy.linalg import norm
from os import pardir, sep
import sys
-from time import sleep
from timeit import timeit
# Modify the system path.
@@ -13,115 +11,44 @@
from lib.geometry.rotations import euler_to_R_zyz
-def proj1(vect, A, N=1, verb=True):
- d = zeros(len(vect), float64)
+def rot1(Ri, R, RT, N=1, verb=True):
+ d = zeros((len(Ri), 3, 3), float64)
for i in range(N):
- for j in xrange(len(vect)):
- d[j] = dot(vect[j], dot(A, vect[j]))
+ for j in xrange(len(Ri)):
+ d[j] = dot(R, dot(Ri[j], RT))
if verb:
- print("\n1st projection - element by element r[i].A.r[i].")
- print("Proj: %s" % d[:2])
+ print("\n1st rotation - element by element R.Ri[i].RT.")
+ print("Rotations:\n%s" % d[:2])
-def proj2(vect, A, N=1, verb=True):
+def rot2(Ri, R, RT, N=1, verb=True):
for i in range(N):
- d = diagonal(tensordot(vect, tensordot(A, transpose(vect), axes=1),
axes=1))
+ d = dot(R, tensordot(Ri, RT, axes=1))
+ d = swapaxes(d, 0, 1)
if verb:
- print("\n2nd projection - diag of double tensordot.")
- print("Proj: %s" % d[:2])
+ print("\n2nd rotation - dot of tensordot, and axis swap.")
+ print("Rotations:\n%s" % d[:2])
-def proj3(vect, A, N=1, verb=True):
- for i in range(N):
- d = diagonal(tensordot(tensordot(A, vect, axes=([0],[1])), vect,
axes=([0],[1])))
- if verb:
- print("\n3rd projection - diag of double tensordot, no transpose.")
- print("Proj: %s" % d[:2])
+# Some 200 3D matrices.
+Ri = array([[1, 2, 3], [2, 3, 4], [3, 4, 5]], float64)
+Ri = tile(Ri, (100, 1, 1))
+if __name__ == '__main__':
+ print("Original matrices:\n%s\nShape: %s" % (Ri[:2], Ri.shape))
-
-def proj4(vect, A, N=1, verb=True):
- d = zeros(len(vect), float64)
- for i in range(N):
- a = tensordot(A, vect, axes=([0],[1]))
- for j in range(len(vect)):
- d[j] = dot(vect[j], a[:,j])
- if verb:
- print("\n4th projection - mixed tensordot() and per-vector dot().")
- print("Proj: %s" % d[:2])
-
-
-def proj5(vect, A, N=1, verb=True):
- d = zeros(len(vect), float64)
- for i in range(N):
- vect2 = vect**2
- double_vect = 2.0 * vect
- for j in xrange(len(vect)):
- d[j] = vect2[j][0]*A[0, 0] + vect2[j][1]*A[1, 1] +
vect2[j][2]*(A[2, 2]) + double_vect[j][0]*vect[j][1]*A[0, 1] +
double_vect[j][0]*vect[j][2]*A[0, 2] + double_vect[j][1]*vect[j][2]*A[1, 2]
- if verb:
- print("\n5th projection - expansion and sum.")
- print("Proj: %s" % d[:2])
-
-
-def proj6(vect, A, N=1, verb=True):
- d = zeros(len(vect), float64)
- for i in range(N):
- d = vect[:,0]**2*A[0, 0] + vect[:,1]**2*A[1, 1] + vect[:,2]**2*(A[2,
2]) + 2.0*vect[:,0]*vect[:,1]*A[0, 1] + 2.0*vect[:,0]*vect[:,2]*A[0, 2] +
2.0*vect[:,1]*vect[:,2]*A[1, 2]
- if verb:
- print("\n6th projection - expansion.")
- print("Proj: %s" % d[:2])
-
-
-def proj7(vect, A, N=1, verb=True):
- d = zeros(len(vect), float64)
- for i in range(N):
- vect2 = vect**2
- double_vect = 2.0 * vect
- d = vect2[:,0]*A[0, 0] + vect2[:,1]*A[1, 1] + vect2[:,2]*(A[2, 2]) +
double_vect[:,0]*vect[:,1]*A[0, 1] + double_vect[:,0]*vect[:,2]*A[0, 2] +
double_vect[:,1]*vect[:,2]*A[1, 2]
- if verb:
- print("\n7th projection - expansion with pre-calculation.")
- print("Proj: %s" % d[:2])
-
-
-# Some 200 vectors.
-vect = array([[1, 2, 3], [2, 2, 2]], float64)
-vect = tile(vect, (100, 1))
+# The rotation matrix.
+R = zeros((3, 3), float64)
+RT = transpose(R)
+euler_to_R_zyz(1, 1, 0.5, R)
if __name__ == '__main__':
- print("Original vectors:\n%s\nShape: %s" % (vect[:2], vect.shape))
-
-# Init the alignment tensor.
-A = zeros((3, 3), float64)
-A_5D = [1.42219822168827662867e-04, -1.44543001566521341940e-04,
-7.07796211648713973798e-04, -6.01619494082773244303e-04,
2.02008007072950861996e-04]
-A[0, 0] = A_5D[0]
-A[1, 1] = A_5D[1]
-A[2, 2] = -A_5D[0] -A_5D[1]
-A[0, 1] = A[1, 0] = A_5D[2]
-A[0, 2] = A[2, 0] = A_5D[3]
-A[1, 2] = A[2, 1] = A_5D[4]
-A *= 1e4
-if __name__ == '__main__':
- print("\nTensor:\n%s\n" % A)
+ print("\nR:\n%s\n" % R)
# Projections.
-N = 100
+N = 1000
M = 100
if __name__ == '__main__':
- proj1(vect=vect, A=A, N=1, verb=True)
- print("Timing (s): %s" % timeit("proj1(vect=vect, A=A, N=N,
verb=False)", setup="from tensor_projections import proj1, vect, A, N",
number=M))
+ rot1(Ri=Ri, R=R, RT=RT, N=1, verb=True)
+ print("Timing (s): %s" % timeit("rot1(Ri=Ri, R=R, RT=RT, N=N,
verb=False)", setup="from frame_rotations import rot1, Ri, R, RT, N",
number=M))
- proj2(vect=vect, A=A, N=1, verb=True)
- print("Timing (s): %s" % timeit("proj2(vect=vect, A=A, N=N,
verb=False)", setup="from tensor_projections import proj2, vect, A, N",
number=M))
-
- proj3(vect=vect, A=A, N=1, verb=True)
- print("Timing (s): %s" % timeit("proj3(vect=vect, A=A, N=N,
verb=False)", setup="from tensor_projections import proj3, vect, A, N",
number=M))
-
- proj4(vect=vect, A=A, N=1, verb=True)
- print("Timing (s): %s" % timeit("proj4(vect=vect, A=A, N=N,
verb=False)", setup="from tensor_projections import proj4, vect, A, N",
number=M))
-
- proj5(vect=vect, A=A, N=1, verb=True)
- print("Timing (s): %s" % timeit("proj5(vect=vect, A=A, N=N,
verb=False)", setup="from tensor_projections import proj5, vect, A, N",
number=M))
-
- proj6(vect=vect, A=A, N=1, verb=True)
- print("Timing (s): %s" % timeit("proj6(vect=vect, A=A, N=N,
verb=False)", setup="from tensor_projections import proj6, vect, A, N",
number=M))
-
- proj7(vect=vect, A=A, N=1, verb=True)
- print("Timing (s): %s" % timeit("proj7(vect=vect, A=A, N=N,
verb=False)", setup="from tensor_projections import proj7, vect, A, N",
number=M))
+ rot2(Ri=Ri, R=R, RT=RT, N=1, verb=True)
+ print("Timing (s): %s" % timeit("rot2(Ri=Ri, R=R, RT=RT, N=N,
verb=False)", setup="from frame_rotations import rot2, Ri, R, RT, N",
number=M))
r23947 - in /branches/frame_order_cleanup/test_suite/shared_data/frame_order/timings: frame_rotations.log frame_rotations.py