Author: bugman
Date: Tue Nov 18 17:50:23 2014
New Revision: 26620
URL: http://svn.gna.org/viewcvs/relax?rev=26620&view=rev
Log:
Expansion of the align_tensor.matrix_angles user function.
The new basis set 'unitary 9D' has been introduced. This creates vectors as
{Sxx, Sxy, Sxz, Syx,
Syy, Syz, Szx, Szy, Szz} and computes the inter-vector angles. These match
the 'matrix' basis set
whereby the Euclidean inner product divided by the Frobenius norms is used to
calculate the
inter-tensor angles.
In addition, the user function documentation and printouts have been
improved. And the backend code
has been simplified.
Modified:
trunk/pipe_control/align_tensor.py
trunk/user_functions/align_tensor.py
Modified: trunk/pipe_control/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/align_tensor.py?rev=26620&r1=26619&r2=26620&view=diff
==============================================================================
--- trunk/pipe_control/align_tensor.py (original)
+++ trunk/pipe_control/align_tensor.py Tue Nov 18 17:50:23 2014
@@ -899,7 +899,7 @@
"""
# Argument check.
- allowed = ['matrix', 'unitary 5D', 'geometric 5D']
+ allowed = ['matrix', 'unitary 9D', 'unitary 5D', 'geometric 5D']
if basis_set not in allowed:
raise RelaxError("The basis set of '%s' is not one of %s." %
(basis_set, allowed))
@@ -915,8 +915,12 @@
tensor_num = tensor_num + 1
# Create the matrix which contains the 5D vectors.
- matrix_3D = zeros((tensor_num, 3, 3), float64)
- matrix_5D = zeros((tensor_num, 5), float64)
+ if basis_set == 'matrix':
+ matrix = zeros((tensor_num, 3, 3), float64)
+ elif basis_set == 'unitary 9D':
+ matrix = zeros((tensor_num, 9), float64)
+ elif basis_set in ['unitary 5D', 'geometric 5D']:
+ matrix = zeros((tensor_num, 5), float64)
# Loop over the tensors.
i = 0
@@ -925,32 +929,41 @@
if tensors and tensor.name not in tensors:
continue
- # Unitary basis set.
+ # Full matrix.
+ if basis_set == 'matrix':
+ matrix[i] = tensor.A
+
+ # 9D unitary basis set.
+ elif basis_set == 'unitary 9D':
+ matrix[i, 0] = tensor.Sxx
+ matrix[i, 1] = tensor.Sxy
+ matrix[i, 2] = tensor.Sxz
+ matrix[i, 3] = tensor.Sxy
+ matrix[i, 4] = tensor.Syy
+ matrix[i, 5] = tensor.Syz
+ matrix[i, 6] = tensor.Sxz
+ matrix[i, 7] = tensor.Syz
+ matrix[i, 8] = tensor.Szz
+
+ # 5D unitary basis set.
if basis_set == 'unitary 5D':
- # Pack the elements.
- matrix_5D[i, 0] = tensor.Sxx
- matrix_5D[i, 1] = tensor.Syy
- matrix_5D[i, 2] = tensor.Sxy
- matrix_5D[i, 3] = tensor.Sxz
- matrix_5D[i, 4] = tensor.Syz
-
- # Geometric basis set.
+ matrix[i, 0] = tensor.Sxx
+ matrix[i, 1] = tensor.Syy
+ matrix[i, 2] = tensor.Sxy
+ matrix[i, 3] = tensor.Sxz
+ matrix[i, 4] = tensor.Syz
+
+ # 5D geometric basis set.
elif basis_set == 'geometric 5D':
- # Pack the elements.
- matrix_5D[i, 0] = tensor.Szz
- matrix_5D[i, 1] = tensor.Sxxyy
- matrix_5D[i, 2] = tensor.Sxy
- matrix_5D[i, 3] = tensor.Sxz
- matrix_5D[i, 4] = tensor.Syz
-
- # Full matrix.
- elif basis_set == 'matrix':
- matrix_3D[i] = tensor.A
+ matrix[i, 0] = tensor.Szz
+ matrix[i, 1] = tensor.Sxxyy
+ matrix[i, 2] = tensor.Sxy
+ matrix[i, 3] = tensor.Sxz
+ matrix[i, 4] = tensor.Syz
# Normalisation.
- if basis_set in ['unitary 5D', 'geometric 5D']:
- norm_5D = linalg.norm(matrix_5D[i])
- matrix_5D[i] = matrix_5D[i] / norm_5D
+ if basis_set in ['unitary 9D', 'unitary 5D', 'geometric 5D']:
+ matrix[i] = matrix[i] / norm(matrix[i])
# Increment the index.
i = i + 1
@@ -960,11 +973,13 @@
# Header printout.
if basis_set == 'matrix':
- sys.stdout.write("Standard inter-matrix angles in degress using the
Euclidean inner product divided by the Frobenius norm")
+ sys.stdout.write("Standard inter-tensor matrix angles in degress
using the Euclidean inner product divided by the Frobenius norms (theta =
arccos(<A1,A2>/(||A1||.||A2||)))")
+ elif basis_set == 'unitary 9D':
+ sys.stdout.write("Inter-tensor vector angles in degrees for the
unitary 9D vectors {Sxx, Sxy, Sxz, Syx, Syy, Syz, Szx, Szy, Szz}")
elif basis_set == 'unitary 5D':
- sys.stdout.write("Inter-matrix angles in degrees for the unitary 5D
vectors {Sxx, Syy, Sxy, Sxz, Syz}")
+ sys.stdout.write("Inter-tensor vector angles in degrees for the
unitary 5D vectors {Sxx, Syy, Sxy, Sxz, Syz}")
elif basis_set == 'geometric 5D':
- sys.stdout.write("Inter-matrix angles in degrees for the geometric
5D vectors {Szz, Sxx-yy, Sxy, Sxz, Syz}")
+ sys.stdout.write("Inter-tensor vector angles in degrees for the
geometric 5D vectors {Szz, Sxx-yy, Sxy, Sxz, Syz}")
sys.stdout.write(":\n\n")
# Initialise the table of data.
@@ -988,10 +1003,10 @@
# Second loop over the columns.
for j in range(tensor_num):
- # The 5D angles.
- if basis_set in ['unitary 5D', 'geometric 5D']:
+ # The vector angles.
+ if basis_set in ['unitary 9D', 'unitary 5D', 'geometric 5D']:
# Dot product.
- delta = dot(matrix_5D[i], matrix_5D[j])
+ delta = dot(matrix[i], matrix[j])
# Check.
if delta > 1:
@@ -1003,10 +1018,10 @@
# The full matrix angle.
elif basis_set in ['matrix']:
# The Euclidean inner product.
- nom = inner(matrix_3D[i].flatten(), matrix_3D[j].flatten())
+ nom = inner(matrix[i].flatten(), matrix[j].flatten())
# The Frobenius norms.
- denom = norm(matrix_3D[i]) * norm(matrix_3D[j])
+ denom = norm(matrix[i]) * norm(matrix[j])
# The angle.
ratio = nom / denom
Modified: trunk/user_functions/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/align_tensor.py?rev=26620&r1=26619&r2=26620&view=diff
==============================================================================
--- trunk/user_functions/align_tensor.py (original)
+++ trunk/user_functions/align_tensor.py Tue Nov 18 17:50:23 2014
@@ -307,8 +307,8 @@
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", "Unitary 5D {Sxx, Syy, Sxy, Sxz, Syz}", "Geometric 5D {Szz, Sxxyy,
Sxy, Sxz, Syz}"],
- wiz_combo_data = ["matrix", "unitary 5D", "geometric 5D"]
+ wiz_combo_choices = ["Standard matrix angles via the Euclidean inner
product", "Unitary 9D {Sxx, Sxy, Sxz, ..., Szz}", "Unitary 5D {Sxx, Syy, Sxy,
Sxz, Syz}", "Geometric 5D {Szz, Sxxyy, Sxy, Sxz, Syz}"],
+ wiz_combo_data = ["matrix", "unitary 9D", "unitary 5D", "geometric 5D"]
)
uf.add_keyarg(
name = "tensors",
@@ -323,9 +323,10 @@
# 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-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("unitary 5D", "The unitary 5D basis set
{Sxx, Syy, Sxy, Sxz, Syz}.")
-uf.desc[-1].add_item_list_element("geometric 5D", "The geometric 5D basis
set {Szz, Sxxyy, Sxy, Sxz, Syz}. This is also the Pales standard notation.")
+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("'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("The full matrix angle via the Euclidean inner
product is defined as:")
uf.desc[-1].add_verbatim("""
/ <A1 , A2> \
r26620 - in /trunk: pipe_control/align_tensor.py user_functions/align_tensor.py