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 This has been replaced by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:")
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