Author: bugman
Date: Tue Sep 23 09:26:08 2014
New Revision: 25961
URL: http://svn.gna.org/viewcvs/relax?rev=25961&view=rev
Log:
Implemented the pseudo-Brownian frame order dynamics simulation for the single
motion models.
This uses the same logic as in the
test_suite/shared_data/frame_order/cam/*/generate_distribution.py
scripts which were used to generate all of the test suite data. However rather
than using a random
rotation matrix, a random 3D vector is used to rotate a fixed angle. And the
rotation is used to
rotate the current state to state i+1. The rotation for the state is
decomposed into torsion-tilt
angles once shifted into the motional eigenframe, the violations checked for as
the state shifted to
the boundary, then the new state reconstructed from the corrected torsion-tilt
angles, and then it
is shifted from the motional eigenframe to the PDB frame.
Modified:
branches/frame_order_cleanup/lib/frame_order/simulation.py
branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
Modified: branches/frame_order_cleanup/lib/frame_order/simulation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/frame_order/simulation.py?rev=25961&r1=25960&r2=25961&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/frame_order/simulation.py (original)
+++ branches/frame_order_cleanup/lib/frame_order/simulation.py Tue Sep 23
09:26:08 2014
@@ -23,14 +23,18 @@
"""Module for simulating the frame order motions."""
# Python module imports.
-from numpy import eye, float64
+from math import cos, pi, sin, sqrt
+from numpy import dot, eye, float64, transpose, zeros
import sys
# relax module imports.
from lib.errors import RelaxError
+from lib.geometry.angles import wrap_angles
+from lib.geometry.rotations import axis_angle_to_R, R_to_tilt_torsion,
tilt_torsion_to_R
+from lib.geometry.vectors import random_unit_vector
-def brownian(file=None, model=None, structure=None, parameters={}, pivot=None,
step_size=2.0, snapshot=10, total=1000):
+def brownian(file=None, model=None, structure=None, parameters={},
eigenframe=None, pivot=None, atom_id=None, step_size=2.0, snapshot=10,
total=1000):
"""Pseudo-Brownian dynamics simulation of the frame order motions.
@keyword file: The opened and writable file object to place the
snapshots into.
@@ -41,8 +45,12 @@
@type model: str
@keyword parameters: The dictionary of model parameter values. The key
is the parameter name and the value is the value.
@type parameters: dict of float
+ @keyword eigenframe: The full 3D eigenframe of the frame order motions.
+ @type eigenframe: numpy rank-2, 3D float64 array
@keyword pivot: The pivot point of the frame order motions.
@type pivot: numpy rank-1, 3D float64 array
+ @keyword atom_id: The atom ID string for the atoms in the structure
to rotate - i.e. the moving domain.
+ @type atom_id: None or str
@keyword step_size: The rotation will be of a random direction but
with this fixed angle. The value is in degrees.
@type step_size: float
@keyword snapshot: The number of steps in the simulation when
snapshots will be taken.
@@ -61,8 +69,34 @@
# The initial state.
state = eye(3, dtype=float64)
- # Initialise the rotation matrix.
+ # Initialise the rotation matrix data structures.
+ vector = zeros(3, float64)
R = eye(3, dtype=float64)
+ step_size = step_size / 360.0 * 2.0 * pi
+
+ # The maximum cone opening angles (isotropic cones).
+ theta_max = None
+ if 'cone_theta_max' in parameters:
+ theta_max = parameters['cone_theta_max']
+
+ # The maximum cone opening angles (isotropic cones).
+ theta_x = None
+ theta_y = None
+ if 'cone_theta_x' in parameters:
+ theta_x = parameters['cone_theta_x']
+ theta_y = parameters['cone_theta_y']
+
+ # The maximum torsion angle.
+ sigma_max = None
+ if 'cone_sigma_max' in parameters:
+ sigma_max = parameters['cone_sigma_max']
+ elif 'free rotor' in model:
+ sigma_max = pi
+
+ # The second torsion angle.
+ sigma_max_2 = None
+ if 'cone_sigma_max_2' in parameters:
+ sigma_max_2 = parameters['cone_sigma_max_2']
# Printout.
print("\nRunning the simulation:")
@@ -75,6 +109,51 @@
if current_snapshot == total:
print("\nEnd of simulation.")
break
+
+ # The random vector.
+ random_unit_vector(vector)
+
+ # The rotation matrix.
+ axis_angle_to_R(vector, step_size, R)
+
+ # Shift the current state.
+ state = dot(R, state)
+
+ # Rotation in the eigenframe.
+ R_eigen = dot(transpose(eigenframe), dot(state, eigenframe))
+
+ # The angles.
+ phi, theta, sigma = R_to_tilt_torsion(R_eigen)
+ sigma = wrap_angles(sigma, -pi, pi)
+
+ # Determine theta_max.
+ if theta_x != None:
+ theta_max = 1.0 / sqrt((cos(phi) / theta_x)**2 + (sin(phi) /
theta_y)**2)
+
+ # Set the cone opening angle to the maximum if outside of the limit.
+ if theta_max != None:
+ if theta > theta_max:
+ theta = theta_max
+
+ # No tilt component.
+ else:
+ theta = 0.0
+ phi = 0.0
+
+ # Set the torsion angle to the maximum if outside of the limits.
+ if sigma_max != None:
+ if sigma > sigma_max:
+ sigma = sigma_max
+ elif sigma < -sigma_max:
+ sigma = -sigma_max
+ else:
+ sigma = 0.0
+
+ # Reconstruct the rotation matrix, in the eigenframe, without sigma.
+ tilt_torsion_to_R(phi, theta, sigma, R_eigen)
+
+ # Rotate back out of the eigenframe.
+ state = dot(eigenframe, dot(R_eigen, transpose(eigenframe)))
# Take a snapshot.
if step == snapshot:
@@ -89,7 +168,7 @@
structure.add_model(model=current_snapshot, coords_from=1)
# Rotate the model.
- structure.rotate(R=R, origin=pivot, model=current_snapshot,
atom_id=None)
+ structure.rotate(R=state, origin=pivot, model=current_snapshot,
atom_id=atom_id)
# Reset the step counter.
step = 0
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=25961&r1=25960&r2=25961&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
23 09:26:08 2014
@@ -40,6 +40,7 @@
from lib.warnings import RelaxWarning
from pipe_control import pipes
from specific_analyses.frame_order.checks import check_domain, check_model,
check_parameters, check_pivot
+from specific_analyses.frame_order.data import domain_moving
from specific_analyses.frame_order.geometric import average_position,
create_ave_pos, create_geometric_rep, generate_axis_system
from specific_analyses.frame_order.optimisation import count_sobol_points
from specific_analyses.frame_order.parameters import assemble_param_vector,
update_model
@@ -407,8 +408,11 @@
# Shift to the average position.
average_position(structure=structure, models=[1])
+ # The motional eigenframe.
+ frame = generate_axis_system()
+
# Create the distribution.
- brownian(file=file, model=cdp.model, structure=structure,
parameters=params, pivot=pivot, step_size=step_size, snapshot=snapshot,
total=total)
+ brownian(file=file, model=cdp.model, structure=structure,
parameters=params, eigenframe=frame, pivot=pivot, atom_id=domain_moving(),
step_size=step_size, snapshot=snapshot, total=total)
# Close the file.
file.close()
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