Author: bugman
Date: Fri Mar 22 23:10:32 2013
New Revision: 19022
URL: http://svn.gna.org/viewcvs/relax?rev=19022&view=rev
Log:
Shifted the maths_fns.alignment_tensor module to lib.nmr.alignment_tensor.
This is part of the relax library redesign.
Added:
trunk/lib/nmr/alignment_tensor.py
- copied unchanged from r19014, trunk/maths_fns/alignment_tensor.py
Removed:
trunk/maths_fns/alignment_tensor.py
Modified:
trunk/lib/nmr/__init__.py
trunk/maths_fns/frame_order/__init__.py
trunk/maths_fns/n_state_model.py
Modified: trunk/lib/nmr/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/nmr/__init__.py?rev=19022&r1=19021&r2=19022&view=diff
==============================================================================
--- trunk/lib/nmr/__init__.py (original)
+++ trunk/lib/nmr/__init__.py Fri Mar 22 23:10:32 2013
@@ -23,5 +23,5 @@
"""The relax-lib NMR package - a library of functions for NMR."""
__all__ = [
- ''
+ 'alignment_tensor'
]
Removed: trunk/maths_fns/alignment_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/maths_fns/alignment_tensor.py?rev=19021&view=auto
==============================================================================
--- trunk/maths_fns/alignment_tensor.py (original)
+++ trunk/maths_fns/alignment_tensor.py (removed)
@@ -1,177 +1,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2008 Edward d'Auvergne
#
-#
#
-# This file is part of the program relax (http://www.nmr-relax.com).
#
-#
#
-# This program is free software: you can redistribute it and/or modify
#
-# it under the terms of the GNU General Public License as published by
#
-# the Free Software Foundation, either version 3 of the License, or
#
-# (at your option) any later version.
#
-#
#
-# This program is distributed in the hope that it will be useful,
#
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
-# GNU General Public License for more details.
#
-#
#
-# You should have received a copy of the GNU General Public License
#
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
-#
#
-###############################################################################
-
-# Module docstring.
-"""Module for the manipulation of alignment tensors."""
-
-# Python imports.
-from numpy.linalg import eigvals
-
-
-def dAi_dAxx(A):
- """The dAi/dAxx gradient.
-
- This function will modify the A matrix to be equal to::
-
- dAi | 1 0 0 |
- ---- = | 0 0 0 |
- dAxx | 0 0 -1 |
-
-
- @param A: The alignment tensor object.
- @type A: numpy rank-2 3D tensor
- """
-
- # Set all elements.
- A[0, 0] = 1.0; A[0, 1] = 0.0; A[0, 2] = 0.0
- A[1, 0] = 0.0; A[1, 1] = 0.0; A[1, 2] = 0.0
- A[2, 0] = 0.0; A[2, 1] = 0.0; A[2, 2] = -1.0
-
-
-def dAi_dAyy(A):
- """The dAi/dAyy gradient.
-
- This function will modify the A matrix to be equal to::
-
- dAi | 0 0 0 |
- ---- = | 0 1 0 |
- dAyy | 0 0 -1 |
-
-
- @param A: The alignment tensor object.
- @type A: numpy rank-2 3D tensor
- """
-
- # Set all elements.
- A[0, 0] = 0.0; A[0, 1] = 0.0; A[0, 2] = 0.0
- A[1, 0] = 0.0; A[1, 1] = 1.0; A[1, 2] = 0.0
- A[2, 0] = 0.0; A[2, 1] = 0.0; A[2, 2] = -1.0
-
-
-def dAi_dAxy(A):
- """The dAi/dAxy gradient.
-
- This function will modify the A matrix to be equal to::
-
- dAi | 0 1 0 |
- ---- = | 1 0 0 |
- dAxy | 0 0 0 |
-
-
- @param A: The alignment tensor object.
- @type A: numpy rank-2 3D tensor
- """
-
- # Set all elements.
- A[0, 0] = 0.0; A[0, 1] = 1.0; A[0, 2] = 0.0
- A[1, 0] = 1.0; A[1, 1] = 0.0; A[1, 2] = 0.0
- A[2, 0] = 0.0; A[2, 1] = 0.0; A[2, 2] = 0.0
-
-
-def dAi_dAxz(A):
- """The dAi/dAxz gradient.
-
- This function will modify the A matrix to be equal to::
-
- dAi | 0 0 1 |
- ---- = | 0 0 0 |
- dAxz | 1 0 0 |
-
-
- @param A: The alignment tensor object.
- @type A: numpy rank-2 3D tensor
- """
-
- # Set all elements.
- A[0, 0] = 0.0; A[0, 1] = 0.0; A[0, 2] = 1.0
- A[1, 0] = 0.0; A[1, 1] = 0.0; A[1, 2] = 0.0
- A[2, 0] = 1.0; A[2, 1] = 0.0; A[2, 2] = 0.0
-
-
-def dAi_dAyz(A):
- """The dAi/dAyz gradient.
-
- This function will modify the A matrix to be equal to::
-
- dAi | 0 0 0 |
- ---- = | 0 0 1 |
- dAyz | 0 1 0 |
-
-
- @param A: The alignment tensor object.
- @type A: numpy rank-2 3D tensor
- """
-
- # Set all elements.
- A[0, 0] = 0.0; A[0, 1] = 0.0; A[0, 2] = 0.0
- A[1, 0] = 0.0; A[1, 1] = 0.0; A[1, 2] = 1.0
- A[2, 0] = 0.0; A[2, 1] = 1.0; A[2, 2] = 0.0
-
-
-def maxA(tensor):
- """Find the maximal alignment - the Azz component in the alignment frame.
-
- @param tensor: The alignment tensor object.
- @type tensor: numpy rank-2 3D tensor
- @return: The Azz component in the alignment frame.
- """
-
- # Return the value.
- return max(abs(eigvals(tensor)))
-
-
-def to_5D(vector_5D, tensor):
- """Convert the rank-2 3D alignment tensor matrix to the 5D vector format.
-
- @param vector_5D: The 5D vector object to populate. The vector format
is {Axx, Ayy, Axy, Axz,
- Ayz}.
- @type vector_5D: numpy 5D vector
- @param tensor: The alignment tensor object.
- @type tensor: numpy rank-2 3D tensor
- """
-
- # Convert the matrix form to the vector form.
- vector_5D[0] = tensor[0, 0]
- vector_5D[1] = tensor[1, 1]
- vector_5D[2] = tensor[0, 1]
- vector_5D[3] = tensor[0, 2]
- vector_5D[4] = tensor[1, 2]
-
-
-def to_tensor(tensor, vector_5D):
- """Convert the 5D vector alignment tensor form to the rank-2 3D matrix
from.
-
- @param tensor: The alignment tensor object, in matrix format, to
populate.
- @type tensor: numpy rank-2 3D tensor
- @param vector_5D: The 5D vector object. The vector format is {Axx,
Ayy, Axy, Axz, Ayz}.
- @type vector_5D: numpy 5D vector
- """
-
- # Convert the vector form to the matrix form.
- tensor[0, 0] = vector_5D[0]
- tensor[0, 1] = vector_5D[2]
- tensor[0, 2] = vector_5D[3]
- tensor[1, 0] = vector_5D[2]
- tensor[1, 1] = vector_5D[1]
- tensor[1, 2] = vector_5D[4]
- tensor[2, 0] = vector_5D[3]
- tensor[2, 1] = vector_5D[4]
- tensor[2, 2] = -vector_5D[0] -vector_5D[1]
Modified: trunk/maths_fns/frame_order/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/maths_fns/frame_order/__init__.py?rev=19022&r1=19021&r2=19022&view=diff
==============================================================================
--- trunk/maths_fns/frame_order/__init__.py (original)
+++ trunk/maths_fns/frame_order/__init__.py Fri Mar 22 23:10:32 2013
@@ -32,7 +32,7 @@
from float import isNaN
from generic_fns.frame_order import print_frame_order_2nd_degree
from extern.sobol.sobol_lib import i4_sobol
-from maths_fns.alignment_tensor import to_5D, to_tensor
+from lib.nmr.alignment_tensor import to_5D, to_tensor
from maths_fns.chi2 import chi2
from maths_fns.coord_transform import spherical_to_cartesian
from maths_fns.frame_order.matrix_ops import Data, reduce_alignment_tensor
Modified: trunk/maths_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/maths_fns/n_state_model.py?rev=19022&r1=19021&r2=19022&view=diff
==============================================================================
--- trunk/maths_fns/n_state_model.py (original)
+++ trunk/maths_fns/n_state_model.py Fri Mar 22 23:10:32 2013
@@ -25,7 +25,7 @@
# relax module imports.
from float import isNaN
-from maths_fns.alignment_tensor import dAi_dAxx, dAi_dAyy, dAi_dAxy,
dAi_dAxz, dAi_dAyz, to_tensor
+from lib.nmr.alignment_tensor import dAi_dAxx, dAi_dAyy, dAi_dAxy, dAi_dAxz,
dAi_dAyz, to_tensor
from maths_fns.chi2 import chi2, dchi2_element, d2chi2_element
from maths_fns.paramag_centre import vectors_single_centre,
vectors_centre_per_state
from maths_fns.pcs import ave_pcs_tensor, ave_pcs_tensor_ddeltaij_dAmn,
ave_pcs_tensor_ddeltaij_dc, pcs_constant_grad, pcs_tensor
r19022 - in /trunk: lib/nmr/ maths_fns/ maths_fns/frame_order/