Author: bugman
Date: Sat Mar 23 10:11:02 2013
New Revision: 19051
URL: http://svn.gna.org/viewcvs/relax?rev=19051&view=rev
Log:
Shifted the target_functions.order_parameters module to
lib.order.order_parameters.
Added:
trunk/lib/order/order_parameters.py
- copied unchanged from r19029,
trunk/target_functions/order_parameters.py
Removed:
trunk/target_functions/order_parameters.py
Modified:
trunk/lib/order/__init__.py
trunk/target_functions/__init__.py
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order.py
trunk/test_suite/system_tests/scripts/frame_order/cam/iso_cone_free_rotor.py
trunk/test_suite/system_tests/scripts/frame_order/cam/iso_cone_free_rotor2.py
trunk/test_suite/system_tests/scripts/frame_order/model_calcs/iso_cone_free_rotor.py
trunk/test_suite/system_tests/scripts/frame_order/model_calcs/iso_cone_free_rotor_eigenframe.py
trunk/test_suite/unit_tests/_target_functions/_frame_order/test_matrix_ops.py
Modified: trunk/lib/order/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/order/__init__.py?rev=19051&r1=19050&r2=19051&view=diff
==============================================================================
--- trunk/lib/order/__init__.py (original)
+++ trunk/lib/order/__init__.py Sat Mar 23 10:11:02 2013
@@ -23,5 +23,5 @@
"""The relax-lib NMR package - a library of functions for order and
entropy."""
__all__ = [
- ''
+ 'order_parameters'
]
Modified: trunk/target_functions/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/__init__.py?rev=19051&r1=19050&r2=19051&view=diff
==============================================================================
--- trunk/target_functions/__init__.py (original)
+++ trunk/target_functions/__init__.py Sat Mar 23 10:11:02 2013
@@ -32,7 +32,6 @@
'jw_mapping',
'mf',
'n_state_model',
- 'order_parameters',
'paramag_centre',
'potential',
'ri_comps',
Removed: trunk/target_functions/order_parameters.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/order_parameters.py?rev=19050&view=auto
==============================================================================
--- trunk/target_functions/order_parameters.py (original)
+++ trunk/target_functions/order_parameters.py (removed)
@@ -1,80 +1,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2010 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 conversion of order parameters to specific model
parameters and vice versa."""
-
-# Python module imports.
-from math import acos, cos, pi, sqrt
-
-
-def iso_cone_theta_to_S(theta):
- """Convert the isotropic cone angle to the order parameter S.
-
- This uses Woessner's diffusion in a cone order parameter defined as::
-
- S = 1/2 (1 + cos(theta)) * cos(theta)
-
-
- @param theta: The isotropic cone angle.
- @type theta: float
- @return: The order parameter value.
- @rtype: float
- """
-
- # Convert.
- S = 0.5 * (1.0 + cos(theta)) * cos(theta)
-
- # Return the order parameter.
- return S
-
-
-def iso_cone_S_to_theta(S):
- """Convert the isotropic cone order parameter S into the cone angle.
-
- This uses Woessner's diffusion in a cone order parameter defined as::
-
- S = 1/2 (1 + cos(theta)) * cos(theta)
-
- The conversion equation is::
-
- theta = acos((sqrt(8.0*S + 1) - 1)/2)
-
- Hence the cone angle is only between 0 and 2pi/3, as the order parameter
for higher cone angles is ambiguous.
-
-
- @param S: The order parameter value (not squared).
- @type S: float
- @return: The value of cos(theta).
- @rtype: float
- """
-
- # Catch bad order parameters.
- if S > 1.0:
- return 0.0
- if S < -0.125:
- return 2*pi
-
- # Convert.
- theta = acos(0.5*(sqrt(8.0*S + 1) - 1))
-
- # Return theta.
- return theta
Modified:
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.py?rev=19051&r1=19050&r2=19051&view=diff
==============================================================================
---
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.py
(original)
+++
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.py
Sat Mar 23 10:11:02 2013
@@ -5,8 +5,8 @@
from os import sep
# relax module imports.
-from target_functions.order_parameters import iso_cone_theta_to_S
from lib.geometry.rotations import euler_to_R_zyz
+from lib.order.order_parameters import iso_cone_theta_to_S
class Analysis:
Modified:
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order.py?rev=19051&r1=19050&r2=19051&view=diff
==============================================================================
---
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order.py
(original)
+++
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order.py
Sat Mar 23 10:11:02 2013
@@ -6,7 +6,7 @@
# relax module imports.
from lib.geometry.rotations import euler_to_R_zyz
-from target_functions.order_parameters import iso_cone_theta_to_S
+from lib.order.order_parameters import iso_cone_theta_to_S
class Analysis:
Modified:
trunk/test_suite/system_tests/scripts/frame_order/cam/iso_cone_free_rotor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/frame_order/cam/iso_cone_free_rotor.py?rev=19051&r1=19050&r2=19051&view=diff
==============================================================================
---
trunk/test_suite/system_tests/scripts/frame_order/cam/iso_cone_free_rotor.py
(original)
+++
trunk/test_suite/system_tests/scripts/frame_order/cam/iso_cone_free_rotor.py
Sat Mar 23 10:11:02 2013
@@ -24,8 +24,8 @@
# relax module imports.
from base_script import Base_script
-from target_functions.order_parameters import iso_cone_theta_to_S
from lib.geometry.rotations import reverse_euler_zyz
+from lib.order.order_parameters import iso_cone_theta_to_S
class Analysis(Base_script):
Modified:
trunk/test_suite/system_tests/scripts/frame_order/cam/iso_cone_free_rotor2.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/frame_order/cam/iso_cone_free_rotor2.py?rev=19051&r1=19050&r2=19051&view=diff
==============================================================================
---
trunk/test_suite/system_tests/scripts/frame_order/cam/iso_cone_free_rotor2.py
(original)
+++
trunk/test_suite/system_tests/scripts/frame_order/cam/iso_cone_free_rotor2.py
Sat Mar 23 10:11:02 2013
@@ -24,8 +24,8 @@
# relax module imports.
from base_script import Base_script
-from target_functions.order_parameters import iso_cone_theta_to_S
from lib.geometry.rotations import reverse_euler_zyz
+from lib.order.order_parameters import iso_cone_theta_to_S
class Analysis(Base_script):
Modified:
trunk/test_suite/system_tests/scripts/frame_order/model_calcs/iso_cone_free_rotor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/frame_order/model_calcs/iso_cone_free_rotor.py?rev=19051&r1=19050&r2=19051&view=diff
==============================================================================
---
trunk/test_suite/system_tests/scripts/frame_order/model_calcs/iso_cone_free_rotor.py
(original)
+++
trunk/test_suite/system_tests/scripts/frame_order/model_calcs/iso_cone_free_rotor.py
Sat Mar 23 10:11:02 2013
@@ -8,7 +8,7 @@
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
from lib.geometry.coord_transform import cartesian_to_spherical
-from target_functions.order_parameters import iso_cone_theta_to_S
+from lib.order.order_parameters import iso_cone_theta_to_S
from status import Status; status = Status()
Modified:
trunk/test_suite/system_tests/scripts/frame_order/model_calcs/iso_cone_free_rotor_eigenframe.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/frame_order/model_calcs/iso_cone_free_rotor_eigenframe.py?rev=19051&r1=19050&r2=19051&view=diff
==============================================================================
---
trunk/test_suite/system_tests/scripts/frame_order/model_calcs/iso_cone_free_rotor_eigenframe.py
(original)
+++
trunk/test_suite/system_tests/scripts/frame_order/model_calcs/iso_cone_free_rotor_eigenframe.py
Sat Mar 23 10:11:02 2013
@@ -8,7 +8,7 @@
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
from lib.geometry.rotations import R_to_euler_zyz
-from target_functions.order_parameters import iso_cone_theta_to_S
+from lib.order.order_parameters import iso_cone_theta_to_S
from status import Status; status = Status()
Modified:
trunk/test_suite/unit_tests/_target_functions/_frame_order/test_matrix_ops.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_target_functions/_frame_order/test_matrix_ops.py?rev=19051&r1=19050&r2=19051&view=diff
==============================================================================
---
trunk/test_suite/unit_tests/_target_functions/_frame_order/test_matrix_ops.py
(original)
+++
trunk/test_suite/unit_tests/_target_functions/_frame_order/test_matrix_ops.py
Sat Mar 23 10:11:02 2013
@@ -29,7 +29,7 @@
from lib.geometry.coord_transform import cartesian_to_spherical
from target_functions.frame_order import *
from lib.algebra.kronecker_product import transpose_23
-from target_functions.order_parameters import iso_cone_theta_to_S
+from lib.order.order_parameters import iso_cone_theta_to_S
from status import Status; status = Status()
r19051 - in /trunk: lib/order/ target_functions/ test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/ test_suite/shar...