Author: bugman
Date: Mon Jul 28 15:48:50 2014
New Revision: 24784
URL: http://svn.gna.org/viewcvs/relax?rev=24784&view=rev
Log:
Renamed the lib.frame_order.rotor_axis module to lib.frame_order.conversions.
This module will be used for all sorts of frame order parameter conversions.
Added:
branches/frame_order_cleanup/lib/frame_order/conversions.py
- copied unchanged from r24783,
branches/frame_order_cleanup/lib/frame_order/rotor_axis.py
Removed:
branches/frame_order_cleanup/lib/frame_order/rotor_axis.py
Modified:
branches/frame_order_cleanup/lib/frame_order/__init__.py
branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
branches/frame_order_cleanup/target_functions/frame_order.py
Modified: branches/frame_order_cleanup/lib/frame_order/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/frame_order/__init__.py?rev=24784&r1=24783&r2=24784&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/frame_order/__init__.py (original)
+++ branches/frame_order_cleanup/lib/frame_order/__init__.py Mon Jul 28
15:48:50 2014
@@ -23,6 +23,7 @@
"""The relax-lib NMR package - a library of functions for the frame order
theories."""
__all__ = [
+ 'conversions',
'double_rotor',
'format',
'free_rotor',
@@ -33,6 +34,5 @@
'pseudo_ellipse_free_rotor',
'pseudo_ellipse',
'pseudo_ellipse_torsionless',
- 'rotor',
- 'rotor_axis'
+ 'rotor'
]
Removed: branches/frame_order_cleanup/lib/frame_order/rotor_axis.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/frame_order/rotor_axis.py?rev=24783&view=auto
==============================================================================
--- branches/frame_order_cleanup/lib/frame_order/rotor_axis.py (original)
+++ branches/frame_order_cleanup/lib/frame_order/rotor_axis.py (removed)
@@ -1,131 +0,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2014 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.
-"""Functions for creating or calculating the rotor axis for the frame order
models."""
-
-# Python module imports.
-from numpy import array, cross, dot, float64, zeros
-from numpy.linalg import norm
-
-# relax module imports.
-from lib.geometry.coord_transform import cartesian_to_spherical,
spherical_to_cartesian
-from lib.geometry.rotations import axis_angle_to_R, euler_to_R_zyz
-
-# Module variables.
-R = zeros((3, 3), float64) # A rotation matrix.
-Z_AXIS = array([0, 0, 1], float64)
-
-
-def convert_axis_alpha_to_spherical(alpha=None, pivot=None, point=None):
- """Convert the axis alpha angle to spherical angles theta and phi.
-
- @keyword alpha: The axis alpha angle, defined as the angle between a
vector perpendicular to the pivot-CoM vector in the xy-plane and the rotor
axis.
- @type alpha: float
- @keyword pivot: The pivot point on the rotation axis.
- @type pivot: numpy rank-1 3D array
- @keyword point: The reference point in space.
- @type point: numpy rank-1 3D array
- @return: The theta and phi spherical angles.
- @rtype: float, float
- """
-
- # Create the axis.
- axis = create_rotor_axis_alpha(alpha=alpha, pivot=pivot, point=point)
-
- # Coordinate system transform.
- r, theta, phi = cartesian_to_spherical(axis)
-
- # Return the angles.
- return theta, phi
-
-
-def create_rotor_axis_alpha(alpha=None, pivot=None, point=None):
- """Create the rotor axis from the axis alpha angle.
-
- @keyword alpha: The axis alpha angle, defined as the angle between a
vector perpendicular to the pivot-CoM vector in the xy-plane and the rotor
axis.
- @type alpha: float
- @keyword pivot: The pivot point on the rotation axis.
- @type pivot: numpy rank-1 3D array
- @keyword point: The reference point in space.
- @type point: numpy rank-1 3D array
- @return: The rotor axis as a unit vector.
- @rtype: numpy rank-1 3D float64 array
- """
-
- # The CoM-pivot unit vector - the norm of the system (the pivot is
defined as the point on the axis closest to the point).
- n = point - pivot
- n /= norm(n)
-
- # The vector perpendicular to the CoM-pivot vector and in the xy plane.
- mu_xy = cross(Z_AXIS, n)
- mu_xy /= norm(mu_xy)
-
- # Rotate the vector about the CoM-pivot axis by the angle alpha.
- axis_angle_to_R(n, alpha, R)
- axis = dot(R, mu_xy)
-
- # Return the new axis.
- return axis
-
-
-def create_rotor_axis_euler(alpha=None, beta=None, gamma=None):
- """Create the rotor axis from the Euler angles.
-
- @keyword alpha: The alpha Euler angle in the zyz notation.
- @type alpha: float
- @keyword beta: The beta Euler angle in the zyz notation.
- @type beta: float
- @keyword gamma: The gamma Euler angle in the zyz notation.
- @type gamma: float
- @return: The rotor axis as a unit vector.
- @rtype: numpy rank-1 3D float64 array
- """
-
- # Initialise the 3D frame.
- frame = zeros((3, 3), float64)
-
- # Euler angle to rotation matrix conversion.
- euler_to_R_zyz(alpha, beta, gamma, frame)
-
- # Return the z-axis component.
- return frame[:, 2]
-
-
-def create_rotor_axis_spherical(theta=None, phi=None):
- """Create the rotor axis from the spherical coordinates.
-
- @keyword theta: The polar spherical angle.
- @type theta: float
- @keyword phi: The azimuthal spherical angle.
- @type phi: float
- @return: The rotor axis as a unit vector.
- @rtype: numpy rank-1 3D float64 array
- """
-
- # Initialise the axis.
- axis = zeros(3, float64)
-
- # Parameter conversion.
- spherical_to_cartesian([1.0, theta, phi], axis)
-
- # Return the new axis.
- return axis
Modified:
branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py?rev=24784&r1=24783&r2=24784&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
(original)
+++ branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
Mon Jul 28 15:48:50 2014
@@ -29,7 +29,7 @@
import sys
# relax module imports.
-from lib.frame_order.rotor_axis import create_rotor_axis_alpha,
create_rotor_axis_euler, create_rotor_axis_spherical
+from lib.frame_order.conversions import create_rotor_axis_alpha,
create_rotor_axis_euler, create_rotor_axis_spherical
from lib.geometry.rotations import euler_to_R_zyz, two_vect_to_R
from lib.io import open_write_file
from lib.order import order_parameters
Modified: branches/frame_order_cleanup/target_functions/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/target_functions/frame_order.py?rev=24784&r1=24783&r2=24784&view=diff
==============================================================================
--- branches/frame_order_cleanup/target_functions/frame_order.py
(original)
+++ branches/frame_order_cleanup/target_functions/frame_order.py Mon
Jul 28 15:48:50 2014
@@ -35,6 +35,7 @@
from lib.compat import norm
from lib.errors import RelaxError
from lib.float import isNaN
+from lib.frame_order.conversions import create_rotor_axis_alpha
from lib.frame_order.double_rotor import compile_2nd_matrix_double_rotor,
pcs_numeric_int_double_rotor
from lib.frame_order.free_rotor import compile_2nd_matrix_free_rotor
from lib.frame_order.iso_cone import compile_2nd_matrix_iso_cone,
pcs_numeric_int_iso_cone_qrint
@@ -45,7 +46,6 @@
from lib.frame_order.pseudo_ellipse_free_rotor import
compile_2nd_matrix_pseudo_ellipse_free_rotor
from lib.frame_order.pseudo_ellipse_torsionless import
compile_2nd_matrix_pseudo_ellipse_torsionless,
pcs_numeric_int_pseudo_ellipse_torsionless_qrint
from lib.frame_order.rotor import compile_2nd_matrix_rotor,
pcs_numeric_int_rotor_qrint
-from lib.frame_order.rotor_axis import create_rotor_axis_alpha
from lib.geometry.coord_transform import spherical_to_cartesian
from lib.geometry.rotations import euler_to_R_zyz, tilt_torsion_to_R,
two_vect_to_R
from lib.linear_algebra.kronecker_product import kron_prod
r24784 - in /branches/frame_order_cleanup: lib/frame_order/ specific_analyses/frame_order/ target_functions/