Author: bugman
Date: Fri Jun 6 10:30:45 2014
New Revision: 23684
URL: http://svn.gna.org/viewcvs/relax?rev=23684&view=rev
Log:
Parameter conversion for all of the CaM free rotor test data frame_order.py
optimisation scripts.
The rotor axis spherical angles have been replaced by the axis alpha angle
defining the rotor with
respect to the xy-plane.
Modified:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor/frame_order.py
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order.py
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order.py
Modified:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor/frame_order.py?rev=23684&r1=23683&r2=23684&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor/frame_order.py
(original)
+++
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor/frame_order.py
Fri Jun 6 10:30:45 2014
@@ -1,7 +1,46 @@
# Script for optimising the free rotor frame order test model of CaM.
# Python module imports.
-from numpy import array
+from numpy import array, cross, float64, zeros
+from numpy.linalg import norm
+
+# relax module imports.
+from lib.frame_order.rotor_axis import create_rotor_axis_alpha
+from lib.geometry.lines import closest_point_ax
+from lib.geometry.coord_transform import spherical_to_cartesian
+from lib.geometry.rotations import reverse_euler_zyz
+from lib.geometry.vectors import vector_angle
+from pipe_control.structure.mass import pipe_centre_of_mass
+
+
+def alpha_angle(pivot=None, com=None, axis=None):
+ """Calculate and return the rotor alpha angle."""
+
+ # The CoM-pivot axis.
+ com_piv = com - pivot
+ com_piv /= norm(com_piv)
+
+ # The mu_xy vector.
+ z_axis = array([0, 0, 1], float64)
+ mu_xy = cross(z_axis, com_piv)
+ mu_xy /= norm(mu_xy)
+
+ # The alpha angle.
+ return vector_angle(mu_xy, axis, com_piv)
+
+
+def shift_pivot(pivot_orig=None, com=None, axis=None):
+ """Shift the pivot to the closest point on the rotor axis to the CoM.)"""
+
+ # The closest point.
+ pivot_new = closest_point_ax(line_pt=pivot_orig, axis=axis, point=com)
+
+ # Printout.
+ print("\n%-20s%s" % ("Original pivot:", pivot_orig))
+ print("%-20s%s" % ("New pivot:", pivot_new))
+
+ # Return the shifted pivot.
+ return pivot_new
# The real parameter values.
@@ -10,6 +49,11 @@
AVE_POS_GAMMA = 4.6622313104265416
AXIS_THETA = 0.9600799785953431
AXIS_PHI = 4.0322755062196229
+
+# Reconstruct the rotation axis.
+AXIS = zeros(3, float64)
+spherical_to_cartesian([1, AXIS_THETA, AXIS_PHI], AXIS)
+print("Rotation axis: %s" % AXIS)
# Create the data pipe.
pipe.create(pipe_name='frame order', pipe_type='frame order')
@@ -71,7 +115,7 @@
frame_order.ref_domain('N')
# Set the initial pivot point.
-pivot = array([ 37.254, 0.5, 16.7465])
+pivot = shift_pivot(pivot_orig=array([ 37.254, 0.5, 16.7465]),
com=pipe_centre_of_mass(verbosity=0), axis=AXIS)
frame_order.pivot(pivot, fix=True)
# Set the paramagnetic centre.
@@ -84,8 +128,7 @@
value.set(param='ave_pos_z', val=AVE_POS_Z)
value.set(param='ave_pos_beta', val=AVE_POS_BETA)
value.set(param='ave_pos_gamma', val=AVE_POS_GAMMA)
-value.set(param='axis_theta', val=AXIS_THETA)
-value.set(param='axis_phi', val=AXIS_PHI)
+value.set(param='axis_alpha', val=alpha_angle(pivot=pivot,
com=pipe_centre_of_mass(verbosity=0), axis=AXIS))
calc()
# Create the PDB representation of the true state.
@@ -93,7 +136,7 @@
# Grid search (low quality for speed).
frame_order.num_int_pts(num=100)
-grid_search(inc=[None, None, None, None, None, 21, 21])
+grid_search(inc=[None, None, None, None, None, 21])
# Iterative optimisation with increasing precision.
num_int_pts = [100, 1000, 10000, 50000]
@@ -112,6 +155,17 @@
for i in range(len(num_int_pts)):
frame_order.num_int_pts(num=num_int_pts[i])
minimise('simplex', func_tol=func_tol[i])
+
+# The distance from the optimised pivot and the rotation axis.
+opt_piv = array([cdp.pivot_x, cdp.pivot_y, cdp.pivot_z])
+print("\n\nOptimised pivot displacement: %s" % norm(pivot - opt_piv))
+pt = closest_point_ax(line_pt=pivot, axis=AXIS, point=opt_piv)
+print("Distance from axis: %s\n" % norm(pt - opt_piv))
+
+# Recreate the axis and compare to the original.
+opt_axis = create_rotor_axis_alpha(alpha=cdp.axis_alpha, pivot=opt_piv,
point=pipe_centre_of_mass(verbosity=0))
+print("Original axis: %s" % AXIS)
+print("Optimised axis: %s" % opt_axis)
# Test Monte Carlo simulations (at low quality for speed).
frame_order.num_int_pts(num=100)
Modified:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order.py?rev=23684&r1=23683&r2=23684&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order.py
(original)
+++
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order.py
Fri Jun 6 10:30:45 2014
@@ -1,7 +1,46 @@
# Script for optimising the second free rotor frame order test model of CaM.
# Python module imports.
-from numpy import array
+from numpy import array, cross, float64, zeros
+from numpy.linalg import norm
+
+# relax module imports.
+from lib.frame_order.rotor_axis import create_rotor_axis_alpha
+from lib.geometry.lines import closest_point_ax
+from lib.geometry.coord_transform import spherical_to_cartesian
+from lib.geometry.rotations import reverse_euler_zyz
+from lib.geometry.vectors import vector_angle
+from pipe_control.structure.mass import pipe_centre_of_mass
+
+
+def alpha_angle(pivot=None, com=None, axis=None):
+ """Calculate and return the rotor alpha angle."""
+
+ # The CoM-pivot axis.
+ com_piv = com - pivot
+ com_piv /= norm(com_piv)
+
+ # The mu_xy vector.
+ z_axis = array([0, 0, 1], float64)
+ mu_xy = cross(z_axis, com_piv)
+ mu_xy /= norm(mu_xy)
+
+ # The alpha angle.
+ return vector_angle(mu_xy, axis, com_piv)
+
+
+def shift_pivot(pivot_orig=None, com=None, axis=None):
+ """Shift the pivot to the closest point on the rotor axis to the CoM.)"""
+
+ # The closest point.
+ pivot_new = closest_point_ax(line_pt=pivot_orig, axis=axis, point=com)
+
+ # Printout.
+ print("\n%-20s%s" % ("Original pivot:", pivot_orig))
+ print("%-20s%s" % ("New pivot:", pivot_new))
+
+ # Return the shifted pivot.
+ return pivot_new
# The real parameter values.
@@ -12,6 +51,11 @@
AVE_POS_GAMMA = 0.09243393677259322
AXIS_THETA = 0.69828059079619353433
AXIS_PHI = 4.03227550621962294031
+
+# Reconstruct the rotation axis.
+AXIS = zeros(3, float64)
+spherical_to_cartesian([1, AXIS_THETA, AXIS_PHI], AXIS)
+print("Rotation axis: %s" % AXIS)
# Create the data pipe.
pipe.create(pipe_name='frame order', pipe_type='frame order')
@@ -73,7 +117,7 @@
frame_order.ref_domain('N')
# Set the initial pivot point.
-pivot = array([ 37.254, 0.5, 16.7465])
+pivot = shift_pivot(pivot_orig=array([ 37.254, 0.5, 16.7465]),
com=pipe_centre_of_mass(verbosity=0), axis=AXIS)
frame_order.pivot(pivot, fix=True)
# Set the paramagnetic centre.
@@ -86,8 +130,7 @@
value.set(param='ave_pos_z', val=AVE_POS_Z)
value.set(param='ave_pos_beta', val=AVE_POS_BETA)
value.set(param='ave_pos_gamma', val=AVE_POS_GAMMA)
-value.set(param='axis_theta', val=AXIS_THETA)
-value.set(param='axis_phi', val=AXIS_PHI)
+value.set(param='axis_alpha', val=alpha_angle(pivot=pivot,
com=pipe_centre_of_mass(verbosity=0), axis=AXIS))
calc()
# Create the PDB representation of the true state.
@@ -95,7 +138,7 @@
# Grid search (low quality for speed).
frame_order.num_int_pts(num=100)
-grid_search(inc=[None, None, None, None, None, 21, 21])
+grid_search(inc=[None, None, None, None, None, 21])
# Iterative optimisation with increasing precision.
num_int_pts = [100, 1000, 10000, 50000]
@@ -114,6 +157,17 @@
for i in range(len(num_int_pts)):
frame_order.num_int_pts(num=num_int_pts[i])
minimise('simplex', func_tol=func_tol[i])
+
+# The distance from the optimised pivot and the rotation axis.
+opt_piv = array([cdp.pivot_x, cdp.pivot_y, cdp.pivot_z])
+print("\n\nOptimised pivot displacement: %s" % norm(pivot - opt_piv))
+pt = closest_point_ax(line_pt=pivot, axis=AXIS, point=opt_piv)
+print("Distance from axis: %s\n" % norm(pt - opt_piv))
+
+# Recreate the axis and compare to the original.
+opt_axis = create_rotor_axis_alpha(alpha=cdp.axis_alpha, pivot=opt_piv,
point=pipe_centre_of_mass(verbosity=0))
+print("Original axis: %s" % AXIS)
+print("Optimised axis: %s" % opt_axis)
# Test Monte Carlo simulations (at low quality for speed).
frame_order.num_int_pts(num=100)
Modified:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order.py?rev=23684&r1=23683&r2=23684&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order.py
(original)
+++
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order.py
Fri Jun 6 10:30:45 2014
@@ -1,7 +1,46 @@
# Script for optimising the free rotor frame order test model of CaM.
# Python module imports.
-from numpy import array
+from numpy import array, cross, float64, zeros
+from numpy.linalg import norm
+
+# relax module imports.
+from lib.frame_order.rotor_axis import create_rotor_axis_alpha
+from lib.geometry.lines import closest_point_ax
+from lib.geometry.coord_transform import spherical_to_cartesian
+from lib.geometry.rotations import reverse_euler_zyz
+from lib.geometry.vectors import vector_angle
+from pipe_control.structure.mass import pipe_centre_of_mass
+
+
+def alpha_angle(pivot=None, com=None, axis=None):
+ """Calculate and return the rotor alpha angle."""
+
+ # The CoM-pivot axis.
+ com_piv = com - pivot
+ com_piv /= norm(com_piv)
+
+ # The mu_xy vector.
+ z_axis = array([0, 0, 1], float64)
+ mu_xy = cross(z_axis, com_piv)
+ mu_xy /= norm(mu_xy)
+
+ # The alpha angle.
+ return vector_angle(mu_xy, axis, com_piv)
+
+
+def shift_pivot(pivot_orig=None, com=None, axis=None):
+ """Shift the pivot to the closest point on the rotor axis to the CoM.)"""
+
+ # The closest point.
+ pivot_new = closest_point_ax(line_pt=pivot_orig, axis=axis, point=com)
+
+ # Printout.
+ print("\n%-20s%s" % ("Original pivot:", pivot_orig))
+ print("%-20s%s" % ("New pivot:", pivot_new))
+
+ # Return the shifted pivot.
+ return pivot_new
# The real parameter values.
@@ -10,6 +49,11 @@
AVE_POS_GAMMA = 4.6622313104265416
AXIS_THETA = 0.9600799785953431
AXIS_PHI = 4.0322755062196229
+
+# Reconstruct the rotation axis.
+AXIS = zeros(3, float64)
+spherical_to_cartesian([1, AXIS_THETA, AXIS_PHI], AXIS)
+print("Rotation axis: %s" % AXIS)
# Create the data pipe.
pipe.create(pipe_name='frame order', pipe_type='frame order')
@@ -73,7 +117,7 @@
frame_order.ref_domain('N')
# Set the initial pivot point.
-pivot = array([ 37.254, 0.5, 16.7465])
+pivot = shift_pivot(pivot_orig=array([ 37.254, 0.5, 16.7465]),
com=pipe_centre_of_mass(verbosity=0), axis=AXIS)
frame_order.pivot(pivot, fix=True)
# Set the paramagnetic centre.
@@ -86,8 +130,7 @@
value.set(param='ave_pos_z', val=AVE_POS_Z)
value.set(param='ave_pos_beta', val=AVE_POS_BETA)
value.set(param='ave_pos_gamma', val=AVE_POS_GAMMA)
-value.set(param='axis_theta', val=AXIS_THETA)
-value.set(param='axis_phi', val=AXIS_PHI)
+value.set(param='axis_alpha', val=alpha_angle(pivot=pivot,
com=pipe_centre_of_mass(verbosity=0), axis=AXIS))
calc()
# Create the PDB representation of the true state.
@@ -95,7 +138,7 @@
# Grid search (low quality for speed).
frame_order.num_int_pts(num=100)
-grid_search(inc=[None, None, None, None, None, 21, 21])
+grid_search(inc=[None, None, None, None, None, 21])
# Iterative optimisation with increasing precision.
num_int_pts = [100, 1000, 10000, 50000]
@@ -114,6 +157,17 @@
for i in range(len(num_int_pts)):
frame_order.num_int_pts(num=num_int_pts[i])
minimise('simplex', func_tol=func_tol[i])
+
+# The distance from the optimised pivot and the rotation axis.
+opt_piv = array([cdp.pivot_x, cdp.pivot_y, cdp.pivot_z])
+print("\n\nOptimised pivot displacement: %s" % norm(pivot - opt_piv))
+pt = closest_point_ax(line_pt=pivot, axis=AXIS, point=opt_piv)
+print("Distance from axis: %s\n" % norm(pt - opt_piv))
+
+# Recreate the axis and compare to the original.
+opt_axis = create_rotor_axis_alpha(alpha=cdp.axis_alpha, pivot=opt_piv,
point=pipe_centre_of_mass(verbosity=0))
+print("Original axis: %s" % AXIS)
+print("Optimised axis: %s" % opt_axis)
# Test Monte Carlo simulations (at low quality for speed).
frame_order.num_int_pts(num=100)
r23684 - in /branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam: free_rotor/ free_rotor2/ free_rotor_missin...