Author: bugman
Date: Tue Sep 9 14:24:13 2014
New Revision: 25713
URL: http://svn.gna.org/viewcvs/relax?rev=25713&view=rev
Log:
Implemented the frame_order.permute_axes user function.
This is used to switch between local minima in the pseudo-elliptic frame
order models.
Modified:
branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
branches/frame_order_cleanup/user_functions/frame_order.py
Modified: branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/frame_order/uf.py?rev=25713&r1=25712&r2=25713&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
(original)
+++ branches/frame_order_cleanup/specific_analyses/frame_order/uf.py Tue
Sep 9 14:24:13 2014
@@ -23,17 +23,19 @@
"""Module for all of the frame order specific user functions."""
# Python module imports.
-from numpy import array, float64
+from numpy import array, float64, transpose, zeros
from warnings import warn
# relax module imports.
from lib.arg_check import is_float_array
+from lib.check_types import is_float
from lib.errors import RelaxError
+from lib.geometry.rotations import euler_to_R_zyz, R_to_euler_zyz
from lib.warnings import RelaxWarning
from pipe_control import pipes
from specific_analyses.frame_order.geometric import create_ave_pos,
create_distribution, create_geometric_rep
from specific_analyses.frame_order.parameters import update_model
-from specific_analyses.frame_order.variables import MODEL_LIST, MODEL_RIGID
+from specific_analyses.frame_order.variables import MODEL_LIST,
MODEL_PSEUDO_ELLIPSE, MODEL_PSEUDO_ELLIPSE_TORSIONLESS, MODEL_RIGID
def num_int_pts(num=200000):
@@ -99,6 +101,42 @@
create_distribution(file=dist, dir=dir, compress_type=compress_type,
force=force)
+def permute_axes():
+ """Permute the axes of the motional eigenframe to switch between local
minima."""
+
+ # Check that the model is valid.
+ if cdp.model not in [MODEL_PSEUDO_ELLIPSE,
MODEL_PSEUDO_ELLIPSE_TORSIONLESS]:
+ raise RelaxError("The permutation of the motional eigenframe is only
valid for the '%s' and '%s' frame order models." % (MODEL_PSEUDO_ELLIPSE,
MODEL_PSEUDO_ELLIPSE_TORSIONLESS))
+
+ # Check that the model parameters are setup.
+ if not hasattr(cdp, 'cone_theta_y') or not is_float(cdp.cone_theta_y):
+ raise RelaxError("The parameter values are not set up.")
+
+ # The angles. Note that cone_theta_x corresponds to a rotation about
the y-axis!
+ angles = array([cdp.cone_theta_y, cdp.cone_theta_x, cdp.cone_sigma_max],
float64)
+
+ # Generate the eigenframe of the motion.
+ frame = zeros((3, 3), float64)
+ euler_to_R_zyz(cdp.eigen_alpha, cdp.eigen_beta, cdp.eigen_gamma, frame)
+
+ # The permutation with the condition that cone_theta_x <= cone_theta_y.
+ if angles[1] <= angles[2]:
+ perm = [2, 0, 1]
+ else:
+ perm = [1, 2, 0]
+
+ # Permute the angles.
+ cdp.cone_theta_y = angles[perm[0]]
+ cdp.cone_theta_x = angles[perm[1]]
+ cdp.cone_sigma_max = angles[perm[2]]
+
+ # Permute the axes.
+ frame_new = transpose(array([frame[:, perm[0]], frame[:, perm[1]],
frame[:, perm[2]]], float64))
+
+ # Convert the permuted frame to Euler angles and store them.
+ cdp.eigen_alpha, cdp.eigen_beta, cdp.eigen_gamma =
R_to_euler_zyz(frame_new)
+
+
def pivot(pivot=None, order=1, fix=False):
"""Set the pivot point for the 2 body motion.
Modified: branches/frame_order_cleanup/user_functions/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/frame_order.py?rev=25713&r1=25712&r2=25713&view=diff
==============================================================================
--- branches/frame_order_cleanup/user_functions/frame_order.py (original)
+++ branches/frame_order_cleanup/user_functions/frame_order.py Tue Sep 9
14:24:13 2014
@@ -24,7 +24,7 @@
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
-from specific_analyses.frame_order.uf import num_int_pts, pdb_model, pivot,
ref_domain, select_model
+from specific_analyses.frame_order.uf import num_int_pts, pdb_model,
permute_axes, pivot, ref_domain, select_model
from specific_analyses.frame_order.variables import MODEL_DOUBLE_ROTOR,
MODEL_FREE_ROTOR, MODEL_ISO_CONE, MODEL_ISO_CONE_FREE_ROTOR,
MODEL_ISO_CONE_TORSIONLESS, MODEL_PSEUDO_ELLIPSE,
MODEL_PSEUDO_ELLIPSE_FREE_ROTOR, MODEL_PSEUDO_ELLIPSE_TORSIONLESS,
MODEL_RIGID, MODEL_ROTOR
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
@@ -128,6 +128,26 @@
uf.gui_icon = "oxygen.actions.document-save"
uf.wizard_height_desc = 400
uf.wizard_size = (1000, 750)
+uf.wizard_image = WIZARD_IMAGE_PATH + 'frame_order.png'
+
+
+# The frame_order.permute_axes user function.
+uf = uf_info.add_uf('frame_order.permute_axes')
+uf.title = "Permute the axes of the motional eigenframe to switch between
local minima."
+uf.title_short = "Eigenframe axis permutation."
+# Description.
+uf.desc.append(Desc_container())
+uf.desc[-1].add_paragraph("The pseudo-elliptic frame order models consist of
multiple solutions as the optimisation space contains multiple local minima.
Because of the constraint cone_theta_x <= cone_theta_y, there are exactly two
local minima. These correspond to permutations of the motional system - the
eigenframe x, y and z-axes as well as the cone opening angles cone_theta_x,
cone_theta_y, and cone_sigma_max associated with these axes are
simultaneously permuted. But as the mechanics of the cone angles is not
identical to that of the torsion angle, only one of the two local minima is
the global minimum.")
+uf.desc[-1].add_paragraph("When optimising the pseudo-elliptic models,
specifically the '%s' and '%s' model, either of the two local minima can be
found. Convergence to the global minimum is not guaranteed. Therefore this
user function can be used to permute the motional system to jump from one
local minimum to the other. Optimisation will be required as the permuted
parameters will not be exactly at the minimum." % (MODEL_PSEUDO_ELLIPSE,
MODEL_PSEUDO_ELLIPSE_TORSIONLESS))
+uf.desc[-1].add_paragraph("The motional system consists of three
permutations but, because of the cone_theta_x <= cone_theta_y condition, the
permutation which causes a violation of this constraint will be skipped.")
+# Prompt examples.
+uf.desc.append(Desc_container("Prompt examples"))
+uf.desc[-1].add_paragraph("Simply type:")
+uf.desc[-1].add_prompt("relax> frame_order.permute_axes()")
+uf.backend = permute_axes
+uf.menu_text = "per&mute_axes"
+uf.wizard_height_desc = 500
+uf.wizard_size = (900, 600)
uf.wizard_image = WIZARD_IMAGE_PATH + 'frame_order.png'
r25713 - in /branches/frame_order_cleanup: specific_analyses/frame_order/uf.py user_functions/frame_order.py