Author: bugman
Date: Fri Jun 13 17:43:50 2014
New Revision: 23943
URL: http://svn.gna.org/viewcvs/relax?rev=23943&view=rev
Log:
Small speed up for all of the frame order models.
The PCS averaging in the quasi-random numerical integration functions now
uses the multiply() and
divide() numpy methods to eliminate a loop over the alignments. For this, a
new dimension over the
spins was added to the PCS constant calculated in the target function
__init__() method. In one
test of the pseudo-ellipse, the time dropped from 191 seconds to 172.
Modified:
branches/frame_order_cleanup/lib/frame_order/double_rotor.py
branches/frame_order_cleanup/lib/frame_order/iso_cone.py
branches/frame_order_cleanup/lib/frame_order/iso_cone_torsionless.py
branches/frame_order_cleanup/lib/frame_order/pseudo_ellipse.py
branches/frame_order_cleanup/lib/frame_order/pseudo_ellipse_torsionless.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=23943&r1=23942&r2=23943&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/frame_order/double_rotor.py
(original)
+++ branches/frame_order_cleanup/lib/frame_order/double_rotor.py Fri
Jun 13 17:43:50 2014
@@ -24,7 +24,7 @@
# Python module imports.
from math import pi, sqrt
-from numpy import dot, inner, sinc, transpose
+from numpy import divide, dot, inner, multiply, sinc, transpose
# relax module imports.
from lib.frame_order.matrix_ops import rotate_daeg
@@ -135,8 +135,8 @@
# Average the PCS.
else:
- for i in range(len(pcs_theta)):
- pcs_theta[i] = c[i] * pcs_theta[i] / float(num)
+ multiply(c, pcs_theta, pcs_theta)
+ 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, R_eigen=None, RT_eigen=None,
Ri_prime=None, pcs_theta=None, pcs_theta_err=None, missing_pcs=None):
Modified: branches/frame_order_cleanup/lib/frame_order/iso_cone.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/frame_order/iso_cone.py?rev=23943&r1=23942&r2=23943&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/frame_order/iso_cone.py (original)
+++ branches/frame_order_cleanup/lib/frame_order/iso_cone.py Fri Jun 13
17:43:50 2014
@@ -24,7 +24,7 @@
# Python module imports.
from math import cos, pi, sqrt
-from numpy import sinc
+from numpy import divide, multiply, sinc
# relax module imports.
from lib.frame_order.matrix_ops import pcs_pivot_motion_full_qrint,
rotate_daeg
@@ -115,8 +115,8 @@
# Average the PCS.
else:
- for i in range(len(pcs_theta)):
- pcs_theta[i] = c[i] * pcs_theta[i] / float(num)
+ multiply(c, pcs_theta, pcs_theta)
+ divide(pcs_theta, float(num), pcs_theta)
def populate_1st_eigenframe_iso_cone(matrix, angle):
Modified: branches/frame_order_cleanup/lib/frame_order/iso_cone_torsionless.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/frame_order/iso_cone_torsionless.py?rev=23943&r1=23942&r2=23943&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/frame_order/iso_cone_torsionless.py
(original)
+++ branches/frame_order_cleanup/lib/frame_order/iso_cone_torsionless.py
Fri Jun 13 17:43:50 2014
@@ -24,6 +24,7 @@
# Python module imports.
from math import cos, sqrt
+from numpy import divide, multiply
# relax module imports.
from lib.frame_order.matrix_ops import pcs_pivot_motion_torsionless_qrint,
rotate_daeg
@@ -134,5 +135,5 @@
# Average the PCS.
else:
- for i in range(len(pcs_theta)):
- pcs_theta[i] = c[i] * pcs_theta[i] / float(num)
+ multiply(c, pcs_theta, pcs_theta)
+ divide(pcs_theta, float(num), pcs_theta)
Modified: branches/frame_order_cleanup/lib/frame_order/pseudo_ellipse.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/frame_order/pseudo_ellipse.py?rev=23943&r1=23942&r2=23943&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/frame_order/pseudo_ellipse.py
(original)
+++ branches/frame_order_cleanup/lib/frame_order/pseudo_ellipse.py Fri
Jun 13 17:43:50 2014
@@ -24,7 +24,7 @@
# Python module imports.
from math import cos, pi, sin, sqrt
-from numpy import sinc
+from numpy import divide, multiply, repeat, sinc, tile
try:
from scipy.integrate import quad
except ImportError:
@@ -659,8 +659,8 @@
# Average the PCS.
else:
- for i in range(len(pcs_theta)):
- pcs_theta[i] = c[i] * pcs_theta[i] / float(num)
+ multiply(c, pcs_theta, pcs_theta)
+ divide(pcs_theta, float(num), pcs_theta)
def tmax_pseudo_ellipse(phi, theta_x, theta_y):
Modified:
branches/frame_order_cleanup/lib/frame_order/pseudo_ellipse_torsionless.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/frame_order/pseudo_ellipse_torsionless.py?rev=23943&r1=23942&r2=23943&view=diff
==============================================================================
---
branches/frame_order_cleanup/lib/frame_order/pseudo_ellipse_torsionless.py
(original)
+++
branches/frame_order_cleanup/lib/frame_order/pseudo_ellipse_torsionless.py
Fri Jun 13 17:43:50 2014
@@ -24,6 +24,7 @@
# Python module imports.
from math import cos, pi, sin, sqrt
+from numpy import divide, multiply
try:
from scipy.integrate import quad
except ImportError:
@@ -320,5 +321,5 @@
# Average the PCS.
else:
- for i in range(len(pcs_theta)):
- pcs_theta[i] = c[i] * pcs_theta[i] / float(num)
+ multiply(c, pcs_theta, pcs_theta)
+ divide(pcs_theta, float(num), pcs_theta)
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=23943&r1=23942&r2=23943&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/frame_order/rotor.py (original)
+++ branches/frame_order_cleanup/lib/frame_order/rotor.py Fri Jun 13
17:43:50 2014
@@ -24,7 +24,7 @@
# Python module imports.
from math import pi, sqrt
-from numpy import dot, inner, sinc, transpose
+from numpy import divide, dot, inner, multiply, sinc, transpose
from numpy.linalg import norm
try:
from scipy.integrate import quad
@@ -136,8 +136,8 @@
# Average the PCS.
else:
- for i in range(len(pcs_theta)):
- pcs_theta[i] = c[i] * pcs_theta[i] / float(num)
+ multiply(c, pcs_theta, pcs_theta)
+ divide(pcs_theta, float(num), pcs_theta)
def pcs_pivot_motion_rotor_qrint(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):
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=23943&r1=23942&r2=23943&view=diff
==============================================================================
--- branches/frame_order_cleanup/target_functions/frame_order.py
(original)
+++ branches/frame_order_cleanup/target_functions/frame_order.py Fri
Jun 13 17:43:50 2014
@@ -270,7 +270,7 @@
# Initialise the data structures.
self.paramag_unit_vect = zeros(atomic_pos.shape, float64)
self.paramag_dist = zeros(self.num_spins, float64)
- self.pcs_const = zeros(self.num_align, float64)
+ self.pcs_const = zeros((self.num_align, self.num_spins), float64)
self.r_pivot_atom = zeros((self.num_spins, 3), float32)
self.r_pivot_atom_rev = zeros((self.num_spins, 3), float32)
self.r_ln_pivot = self.pivot - self.paramag_centre
@@ -1045,7 +1045,7 @@
# The PCS calculation.
vect = self.r_ln_pivot[0] + r_pivot_atom
length = norm(vect)
- self.pcs_theta[align_index, j] =
pcs_tensor(self.pcs_const[align_index] / length**5, vect,
self.A_3D[align_index])
+ self.pcs_theta[align_index, j] =
pcs_tensor(self.pcs_const[align_index, j] / length**5, vect,
self.A_3D[align_index])
# Calculate and sum the single alignment chi-squared value
(for the PCS).
chi2_sum = chi2_sum + chi2(self.pcs[align_index],
self.pcs_theta[align_index], self.pcs_error[align_index])
r23943 - in /branches/frame_order_cleanup: lib/frame_order/ target_functions/