Author: bugman
Date: Mon Nov 10 15:04:26 2014
New Revision: 26481
URL: http://svn.gna.org/viewcvs/relax?rev=26481&view=rev
Log:
Eliminated the lib.frame_order.iso_cone.populate_*() functions.
The populate_1st_eigenframe_iso_cone() function was unused and incorrect, so
it was deleted. The
contents of the populate_2nd_eigenframe_iso_cone() function have been shifted
compile_2nd_matrix_iso_cone() as a separate function is unnecessary. This
now matches all the other
lib.frame_order modules.
Modified:
branches/frame_order_cleanup/lib/frame_order/iso_cone.py
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=26481&r1=26480&r2=26481&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/frame_order/iso_cone.py (original)
+++ branches/frame_order_cleanup/lib/frame_order/iso_cone.py Mon Nov 10
15:04:26 2014
@@ -78,8 +78,40 @@
@type sigma_max: float
"""
- # Populate the Frame Order matrix in the eigenframe.
- populate_2nd_eigenframe_iso_cone(matrix, cone_theta, sigma_max)
+ # Zeros.
+ matrix[:] = 0.0
+
+ # Repetitive trig calculations.
+ sinc_smax = sinc(sigma_max/pi)
+ sinc_2smax = sinc(2.0*sigma_max/pi)
+ cos_tmax = cos(cone_theta)
+ cos_tmax2 = cos_tmax**2
+
+ # Larger factors.
+ fact_sinc_2smax = sinc_2smax*(cos_tmax2 + 4.0*cos_tmax + 7.0) / 24.0
+ fact_cos_tmax2 = (cos_tmax2 + cos_tmax + 4.0) / 12.0
+ fact_cos_tmax = (cos_tmax + 1.0) / 4.0
+
+ # Diagonal.
+ matrix[0, 0] = fact_sinc_2smax + fact_cos_tmax2
+ matrix[1, 1] = fact_sinc_2smax + fact_cos_tmax
+ matrix[2, 2] = sinc_smax * (2.0*cos_tmax2 + 5.0*cos_tmax + 5.0) / 12.0
+ matrix[3, 3] = matrix[1, 1]
+ matrix[4, 4] = matrix[0, 0]
+ matrix[5, 5] = matrix[2, 2]
+ matrix[6, 6] = matrix[2, 2]
+ matrix[7, 7] = matrix[2, 2]
+ matrix[8, 8] = (cos_tmax2 + cos_tmax + 1.0) / 3.0
+
+ # Off diagonal set 1.
+ matrix[0, 4] = matrix[4, 0] = -fact_sinc_2smax + fact_cos_tmax2
+ matrix[0, 8] = matrix[8, 0] = -(cos_tmax2 + cos_tmax - 2.0) / 6.0
+ matrix[4, 8] = matrix[8, 4] = matrix[0, 8]
+
+ # Off diagonal set 2.
+ matrix[1, 3] = matrix[3, 1] = fact_sinc_2smax - fact_cos_tmax
+ matrix[2, 6] = matrix[6, 2] = sinc_smax * (cos_tmax2 + cos_tmax - 2.0) /
6.0
+ matrix[5, 7] = matrix[7, 5] = matrix[2, 6]
# Rotate and return the frame order matrix.
return rotate_daeg(matrix, Rx2_eigen)
@@ -204,71 +236,3 @@
# Return the value.
return c * result[0] / SA
-
-
-def populate_1st_eigenframe_iso_cone(matrix, angle):
- """Populate the 1st degree Frame Order matrix in the eigenframe for an
isotropic cone.
-
- The cone axis is assumed to be parallel to the z-axis in the eigenframe.
-
- @param matrix: The Frame Order matrix, 1st degree.
- @type matrix: numpy 3D, rank-2 array
- @param angle: The cone angle.
- @type angle: float
- """
-
- # Zeros.
- matrix[:] = 0.0
-
- # The c33 element.
- matrix[2, 2] = (cos(angle) + 1.0) / 2.0
-
-
-def populate_2nd_eigenframe_iso_cone(matrix, tmax, smax):
- """Populate the 2nd degree Frame Order matrix in the eigenframe for the
isotropic cone.
-
- The cone axis is assumed to be parallel to the z-axis in the eigenframe.
-
-
- @param matrix: The Frame Order matrix, 2nd degree.
- @type matrix: numpy 9D, rank-2 array
- @param tmax: The cone opening angle.
- @type tmax: float
- @param smax: The maximum torsion angle.
- @type smax: float
- """
-
- # Zeros.
- matrix[:] = 0.0
-
- # Repetitive trig calculations.
- sinc_smax = sinc(smax/pi)
- sinc_2smax = sinc(2.0*smax/pi)
- cos_tmax = cos(tmax)
- cos_tmax2 = cos_tmax**2
-
- # Larger factors.
- fact_sinc_2smax = sinc_2smax*(cos_tmax2 + 4.0*cos_tmax + 7.0) / 24.0
- fact_cos_tmax2 = (cos_tmax2 + cos_tmax + 4.0) / 12.0
- fact_cos_tmax = (cos_tmax + 1.0) / 4.0
-
- # Diagonal.
- matrix[0, 0] = fact_sinc_2smax + fact_cos_tmax2
- matrix[1, 1] = fact_sinc_2smax + fact_cos_tmax
- matrix[2, 2] = sinc_smax * (2.0*cos_tmax2 + 5.0*cos_tmax + 5.0) / 12.0
- matrix[3, 3] = matrix[1, 1]
- matrix[4, 4] = matrix[0, 0]
- matrix[5, 5] = matrix[2, 2]
- matrix[6, 6] = matrix[2, 2]
- matrix[7, 7] = matrix[2, 2]
- matrix[8, 8] = (cos_tmax2 + cos_tmax + 1.0) / 3.0
-
- # Off diagonal set 1.
- matrix[0, 4] = matrix[4, 0] = -fact_sinc_2smax + fact_cos_tmax2
- matrix[0, 8] = matrix[8, 0] = -(cos_tmax2 + cos_tmax - 2.0) / 6.0
- matrix[4, 8] = matrix[8, 4] = matrix[0, 8]
-
- # Off diagonal set 2.
- matrix[1, 3] = matrix[3, 1] = fact_sinc_2smax - fact_cos_tmax
- matrix[2, 6] = matrix[6, 2] = sinc_smax * (cos_tmax2 + cos_tmax - 2.0) /
6.0
- matrix[5, 7] = matrix[7, 5] = matrix[2, 6]
r26481 - /branches/frame_order_cleanup/lib/frame_order/iso_cone.py