Author: bugman
Date: Tue Oct 28 14:23:43 2014
New Revision: 26394
URL: http://svn.gna.org/viewcvs/relax?rev=26394&view=rev
Log:
Replaced the table in the frame_order.permute_axes user function.
The original table was an old and incorrect version. This has been replaced
by the correct
permutation table.
Modified:
branches/frame_order_cleanup/user_functions/frame_order.py
Modified: branches/frame_order_cleanup/user_functions/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/frame_order.py?rev=26394&r1=26393&r2=26394&view=diff
==============================================================================
--- branches/frame_order_cleanup/user_functions/frame_order.py (original)
+++ branches/frame_order_cleanup/user_functions/frame_order.py Tue Oct 28
14:23:43 2014
@@ -179,14 +179,18 @@
uf.desc[-1].add_paragraph("The isotropic and pseudo-elliptic cone frame
order models consist of multiple solutions as the optimisation space contains
multiple local minima. Because of the constraint cone_theta_x <=
cone_theta_y in the pseudo-ellipse model, there are exactly three local
minima (out of 6 possible permutations). However the cone_theta_x ==
cone_theta_y condition of the isotropic cone collapses this to two minima.
The multiple minima correspond to permutations of the motional system - the
eigenframe x, y and z-axes as well as the cone opening angles cone_theta_x,
cone_theta_y, and cone_sigma_max associated with these axes. But as the
mechanics of the cone angles is not identical to that of the torsion angle,
only one of the three local minima is the global minimum.")
uf.desc[-1].add_paragraph("When optimising the pseudo-elliptic models,
specifically the '%s' and '%s' model, any of the three local minima can be
found. Convergence to the global minimum is not guaranteed. Therefore this
user function can be used to permute the motional system to jump from one
local minimum to the other. Optimisation will be required as the permuted
parameters will not be exactly at the minimum." % (MODEL_PSEUDO_ELLIPSE,
MODEL_PSEUDO_ELLIPSE_TORSIONLESS))
table = uf_tables.add_table(label="table: frame_order.permute_axes
combinations", caption="The motional eigenframe permutations for the
frame_order.permute_axes user function.", caption_short="The permutations for
the frame_order.permute_axes user function.")
-table.add_headings(["Permutation ", "Axis inversion", "If x < y < z", "If x
< z < y", "If z < x < y"])
-table.add_row([ "[x', y', z']", " z ", " Self ", "
Self ", " Self "])
-table.add_row([ "[x', z', y']", " -z ", " A ", "
A ", " x "])
-table.add_row([ "[y', x', z']", " -z ", " x ", "
x ", " x "])
-table.add_row([ "[y', z', x']", " z ", " B ", "
x ", " x "])
-table.add_row([ "[z', x', y']", " z ", " x ", "
x ", " A "])
-table.add_row([ "[z', y', x']", " -z ", " x ", "
B ", " B "])
+table.add_headings(["Condition", "Permutation name", "Cone angles", "Axes"])
+table.add_row(["x < y < z", "Self", "[x, y, z]", "[x, y, z]"])
+table.add_row([" ", " A ", "[x, z, y]", "[-z, y, x]"])
+table.add_row([" ", " B ", "[y, z, x]", "[z, x, y]"])
+table.add_row(["x < z < y", "Self", "[x, y, z]", "[x, y, z]"])
+table.add_row([" ", " A ", "[x, z, y]", "[-z, y, x]"])
+table.add_row([" ", " B ", "[z, y, x]", "[x, -z, y]"])
+table.add_row(["z < x < y", "Self", "[x, y, z]", "[x, y, z]"])
+table.add_row([" ", " A ", "[z, x, y]", "[y, z, x]"])
+table.add_row([" ", " B ", "[z, y, x]", "[x, -z, y]"])
uf.desc[-1].add_table(table.label)
+uf.desc[-1].add_paragraph("In this table, the condition and cone angle
values [x, y, z] correspond to cone_theta_x, cone_theta_y, and
cone_sigma_max.")
# Prompt examples.
uf.desc.append(Desc_container("Prompt examples"))
uf.desc[-1].add_paragraph("For combination 'A', simply type:")
r26394 - /branches/frame_order_cleanup/user_functions/frame_order.py