Author: bugman
Date: Wed Nov 19 17:44:46 2014
New Revision: 26628
URL: http://svn.gna.org/viewcvs/relax?rev=26628&view=rev
Log:
Editing of the description for the align_tensor.matrix_angles user function.
Modified:
trunk/user_functions/align_tensor.py
Modified: trunk/user_functions/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/align_tensor.py?rev=26628&r1=26627&r2=26628&view=diff
==============================================================================
--- trunk/user_functions/align_tensor.py (original)
+++ trunk/user_functions/align_tensor.py Wed Nov 19 17:44:46 2014
@@ -307,7 +307,7 @@
desc_short = "basis set",
desc = "The basis set to operate with.",
wiz_element_type = "combo",
- wiz_combo_choices = ["Standard matrix angles via the Euclidean inner
product", "Irreducible 5D {A-2, A-1, A0, A1, A2}", "Unitary 9D {Sxx, Sxy, Sxz,
..., Szz}", "Unitary 5D {Sxx, Syy, Sxy, Sxz, Syz}", "Geometric 5D {Szz, Sxxyy,
Sxy, Sxz, Syz}"],
+ wiz_combo_choices = ["Standard inter-matrix angles", "Irreducible 5D {A-2,
A-1, A0, A1, A2}", "Unitary 9D {Sxx, Sxy, Sxz, ..., Szz}", "Unitary 5D {Sxx,
Syy, Sxy, Sxz, Syz}", "Geometric 5D {Szz, Sxxyy, Sxy, Sxz, Syz}"],
wiz_combo_data = ["matrix", "irreducible 5D", "unitary 9D", "unitary 5D",
"geometric 5D"]
)
uf.add_keyarg(
@@ -322,19 +322,19 @@
)
# Description.
uf.desc.append(Desc_container())
-uf.desc[-1].add_paragraph("This will calculate the inter-matrix angles between
all loaded alignment tensors for the current data pipe. For the 5D basis sets,
the matrices are first converted to a 5D vector form and then then the
inter-vector angles, rather than inter-matrix angles, are calculated. The
angles are dependent upon the basis set:")
-uf.desc[-1].add_item_list_element("'matrix'", "The standard inter-tensor
matrix angle. This is the default option. The angle is calculated via the
Euclidean inner product of the alignment matrices in rank-2, 3D form divided by
the Frobenius norm ||A||_F of the matrices.")
-uf.desc[-1].add_item_list_element("'irreducible 5D'", "The inter-tensor vector
angle for the irreducible 5D basis set {A-2, A-1, A0, A1, A2}.")
-uf.desc[-1].add_item_list_element("'unitary 9D'", "The inter-tensor vector
angle for the unitary 9D basis set {Sxx, Sxy, Sxz, Syx, Syy, Syz, Szx, Szy,
Szz}.")
-uf.desc[-1].add_item_list_element("'unitary 5D'", "The inter-tensor vector
angle for the unitary 5D basis set {Sxx, Syy, Sxy, Sxz, Syz}.")
-uf.desc[-1].add_item_list_element("'geometric 5D'", "The inter-tensor vector
angle for the geometric 5D basis set {Szz, Sxxyy, Sxy, Sxz, Syz}. This is also
the Pales standard notation.")
+uf.desc[-1].add_paragraph("This will calculate the inter-matrix angles between
all loaded alignment tensors for the current data pipe. For the vector basis
sets, the matrices are first converted to vector form and then then the
inter-vector angles rather than inter-matrix angles are calculated. The angles
are dependent upon the basis set - linear maps produce identical results
whereas non-linear map produce result in different angle. The basis set can be
one of:")
+uf.desc[-1].add_item_list_element("'matrix'", "The standard inter-matrix
angles. This default option is a linear map, hence angles are preserved. The
angle is calculated via the arccos of the Euclidean inner product of the
alignment matrices in rank-2, 3D form divided by the Frobenius norm ||A||_F of
the matrices.")
+uf.desc[-1].add_item_list_element("'irreducible 5D'", "The inter-tensor vector
angles for the irreducible 5D basis set {A-2, A-1, A0, A1, A2}. This is a
linear map, hence angles are preserved.")
+uf.desc[-1].add_item_list_element("'unitary 9D'", "The inter-tensor vector
angles for the unitary 9D basis set {Sxx, Sxy, Sxz, Syx, Syy, Syz, Szx, Szy,
Szz}. This is a linear map, hence angles are preserved.")
+uf.desc[-1].add_item_list_element("'unitary 5D'", "The inter-tensor vector
angles for the unitary 5D basis set {Sxx, Syy, Sxy, Sxz, Syz}. This is a
non-linear map, hence angles are not preserved.")
+uf.desc[-1].add_item_list_element("'geometric 5D'", "The inter-tensor vector
angles for the geometric 5D basis set {Szz, Sxxyy, Sxy, Sxz, Syz}. This is a
non-linear map, hence angles are not preserved. This is also the Pales
standard notation.")
uf.desc[-1].add_paragraph("The full matrix angle via the Euclidean inner
product is defined as")
uf.desc[-1].add_verbatim("""\
/ <A1 , A2> \
theta = arccos | ------------- | ,
\ ||A1|| ||A2|| / \
""")
-uf.desc[-1].add_paragraph("where <a,b> is the Euclidean inner product and
||a|| is the Frobenius norm of the matrix. For the irreducible basis set, the
Am components are defined as")
+uf.desc[-1].add_paragraph("where <a,b> is the Euclidean inner product and
||a|| is the Frobenius norm of the matrix. For the irreducible 5D basis set,
the Am components are defined as")
uf.desc[-1].add_verbatim("""\
/ 4pi \ 1/2
A0 = | --- | Szz ,
@@ -361,7 +361,6 @@
m=-2,2 \
""")
uf.desc[-1].add_paragraph("and where Am* = (-1)^m A-m, and the norm is defined
as |A1| = Re(sqrt(<A1|A1>)).")
-uf.desc[-1].add_paragraph("The inner product solution is a linear map and
thereby preserves angles, whereas the {Sxx, Syy, Sxy, Sxz, Syz} and {Szz,
Sxxyy, Sxy, Sxz, Syz} basis sets are non-linear maps which do not preserve
angles. Therefore the angles from all three basis sets will be different.")
uf.backend = align_tensor.matrix_angles
uf.menu_text = "&matrix_angles"
uf.gui_icon = "oxygen.categories.applications-education"
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