Author: bugman
Date: Sat Mar 23 10:38:28 2013
New Revision: 19059
URL: http://svn.gna.org/viewcvs/relax?rev=19059&view=rev
Log:
Shifted the target_functions.paramag_centre module to
lib.alignment.paramag_centre.
Added:
trunk/lib/alignment/paramag_centre.py
- copied unchanged from r19029, trunk/target_functions/paramag_centre.py
Removed:
trunk/target_functions/paramag_centre.py
Modified:
trunk/lib/alignment/__init__.py
trunk/target_functions/__init__.py
trunk/target_functions/n_state_model.py
Modified: trunk/lib/alignment/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/alignment/__init__.py?rev=19059&r1=19058&r2=19059&view=diff
==============================================================================
--- trunk/lib/alignment/__init__.py (original)
+++ trunk/lib/alignment/__init__.py Sat Mar 23 10:38:28 2013
@@ -24,6 +24,7 @@
__all__ = [
'alignment_tensor',
+ 'paramag_centre',
'pcs',
'rdc'
]
Modified: trunk/target_functions/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/__init__.py?rev=19059&r1=19058&r2=19059&view=diff
==============================================================================
--- trunk/target_functions/__init__.py (original)
+++ trunk/target_functions/__init__.py Sat Mar 23 10:38:28 2013
@@ -31,6 +31,5 @@
'jw_mapping',
'mf',
'n_state_model',
- 'paramag_centre',
'potential'
]
Modified: trunk/target_functions/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/n_state_model.py?rev=19059&r1=19058&r2=19059&view=diff
==============================================================================
--- trunk/target_functions/n_state_model.py (original)
+++ trunk/target_functions/n_state_model.py Sat Mar 23 10:38:28 2013
@@ -24,15 +24,15 @@
from numpy import array, dot, eye, float64, ones, rank, transpose, zeros
# relax module imports.
+from target_functions.chi2 import chi2, dchi2_element, d2chi2_element
+from lib.alignment.alignment_tensor import dAi_dAxx, dAi_dAyy, dAi_dAxy,
dAi_dAxz, dAi_dAyz, to_tensor
+from lib.alignment.paramag_centre import vectors_single_centre,
vectors_centre_per_state
+from lib.alignment.pcs import ave_pcs_tensor, ave_pcs_tensor_ddeltaij_dAmn,
ave_pcs_tensor_ddeltaij_dc, pcs_constant_grad, pcs_tensor
+from lib.alignment.rdc import ave_rdc_tensor, ave_rdc_tensor_dDij_dAmn,
rdc_tensor
+from lib.errors import RelaxError, RelaxImplementError
from lib.float import isNaN
-from lib.alignment.alignment_tensor import dAi_dAxx, dAi_dAyy, dAi_dAxy,
dAi_dAxz, dAi_dAyz, to_tensor
-from target_functions.chi2 import chi2, dchi2_element, d2chi2_element
-from target_functions.paramag_centre import vectors_single_centre,
vectors_centre_per_state
-from lib.alignment.pcs import ave_pcs_tensor, ave_pcs_tensor_ddeltaij_dAmn,
ave_pcs_tensor_ddeltaij_dc, pcs_constant_grad, pcs_tensor
from lib.geometry.rotations import euler_to_R_zyz
-from lib.alignment.rdc import ave_rdc_tensor, ave_rdc_tensor_dDij_dAmn,
rdc_tensor
from lib.physical_constants import pcs_constant
-from lib.errors import RelaxError, RelaxImplementError
class N_state_opt:
Removed: trunk/target_functions/paramag_centre.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/paramag_centre.py?rev=19058&view=auto
==============================================================================
--- trunk/target_functions/paramag_centre.py (original)
+++ trunk/target_functions/paramag_centre.py (removed)
@@ -1,92 +1,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2010-2011 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 functions relating to the paramagnetic centre."""
-
-# Python imports.
-from numpy.linalg import norm
-
-
-def vectors_centre_per_state(atomic_pos, paramag_centre, unit_vector, r):
- """Calculate the electron spin to nuclear spin unit vectors and
distances.
-
- This assumes that there is one paramagnetic centre per state of the
system.
-
-
- @param atomic_pos: The atomic positions in Angstrom. The first
index is the spins, the second is the structures, and the third is the atomic
coordinates.
- @type atomic_pos: numpy rank-3 array
- @param paramag_centre: The paramagnetic centre position in Angstrom.
- @type paramag_centre: numpy rank-2, Nx3 array
- @param unit_vector: The structure to fill with the electron spin to
nuclear spin unit vectors.
- @type unit_vector: numpy rank-3 array
- @param r: The structure to fill with the electron spin to
nuclear spin distances.
- @type r: numpy rank-2 array
- """
-
- # Loop over the spins.
- for i in range(len(atomic_pos)):
- # Loop over the states.
- for c in range(len(atomic_pos[i])):
- # The vector.
- vect = atomic_pos[i, c] - paramag_centre[c]
-
- # The length.
- r[i, c] = norm(vect)
-
- # The unit vector.
- unit_vector[i, c] = vect / r[i, c]
-
- # Convert the distances from Angstrom to meters.
- r[i, c] = r[i, c] * 1e-10
-
-
-def vectors_single_centre(atomic_pos, paramag_centre, unit_vector, r):
- """Calculate the electron spin to nuclear spin unit vectors and
distances.
-
- This assumes that there is only one paramagnetic centre for all states
of the system.
-
-
- @param atomic_pos: The atomic positions in Angstrom. The first
index is the spins, the second is the structures, and the third is the atomic
coordinates.
- @type atomic_pos: numpy rank-3 array
- @param paramag_centre: The paramagnetic centre position in Angstrom.
- @type paramag_centre: numpy rank-1, 3D array
- @param unit_vector: The structure to fill with the electron spin to
nuclear spin unit vectors.
- @type unit_vector: numpy rank-3 array
- @param r: The structure to fill with the electron spin to
nuclear spin distances.
- @type r: numpy rank-2 array
- """
-
- # Loop over the spins.
- for i in range(len(atomic_pos)):
- # Loop over the states.
- for c in range(len(atomic_pos[i])):
- # The vector.
- vect = atomic_pos[i, c] - paramag_centre
-
- # The length.
- r[i, c] = norm(vect)
-
- # The unit vector.
- unit_vector[i, c] = vect / r[i, c]
-
- # Convert the distances from Angstrom to meters.
- r[i, c] = r[i, c] * 1e-10
r19059 - in /trunk: lib/alignment/ target_functions/