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"