Author: bugman
Date: Wed Sep 24 13:25:34 2014
New Revision: 26003
URL: http://svn.gna.org/viewcvs/relax?rev=26003&view=rev
Log:
Updated all of the SciPy quadratic integration frame order target functions.
The pivot point is now handled quite different from back in May when these
functions were deleted.
Modified:
branches/frame_order_cleanup/target_functions/frame_order.py
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=26003&r1=26002&r2=26003&view=diff
==============================================================================
--- branches/frame_order_cleanup/target_functions/frame_order.py
(original)
+++ branches/frame_order_cleanup/target_functions/frame_order.py Wed Sep
24 13:25:34 2014
@@ -559,15 +559,16 @@
# Unpack the parameters.
if self.pivot_opt:
- self._param_pivot = params[:3]
+ pivot = outer(self.spin_ones_struct, params[:3])
self._translation_vector = params[3:6]
- ave_pos_beta, ave_pos_gamma, axis_theta, axis_phi = params[6:]
+ ave_pos_beta, ave_pos_gamma, axis_alpha = params[6:]
else:
+ pivot = self.pivot
self._translation_vector = params[:3]
- ave_pos_beta, ave_pos_gamma, axis_theta, axis_phi = params[3:]
-
- # Generate the cone axis from the spherical angles.
- spherical_to_cartesian([1.0, axis_theta, axis_phi], self.cone_axis)
+ ave_pos_beta, ave_pos_gamma, axis_alpha = params[3:]
+
+ # Generate the rotor axis.
+ self.cone_axis = create_rotor_axis_alpha(alpha=axis_alpha,
pivot=pivot[0], point=self.com)
# Pre-calculate the eigenframe rotation matrix.
two_vect_to_R(self.z_axis, self.cone_axis, self.R_eigen)
@@ -587,7 +588,7 @@
# Pre-calculate all the necessary vectors.
if self.pcs_flag:
- self.calc_vectors(self._param_pivot, self.R_ave, RT_ave)
+ self.calc_vectors(pivot=pivot, R_ave=self.R_ave, RT_ave=RT_ave)
# Initial chi-squared (or SSE) value.
chi2_sum = 0.0
@@ -723,10 +724,11 @@
# Unpack the parameters.
if self.pivot_opt:
- self._param_pivot = params[:3]
+ pivot = outer(self.spin_ones_struct, params[:3])
self._translation_vector = params[3:6]
ave_pos_alpha, ave_pos_beta, ave_pos_gamma, axis_theta, axis_phi,
cone_theta, sigma_max = params[6:]
else:
+ pivot = self.pivot
self._translation_vector = params[:3]
ave_pos_alpha, ave_pos_beta, ave_pos_gamma, axis_theta, axis_phi,
cone_theta, sigma_max = params[3:]
@@ -751,7 +753,7 @@
# Pre-calculate all the necessary vectors.
if self.pcs_flag:
- self.calc_vectors(self._param_pivot, self.R_ave, RT_ave)
+ self.calc_vectors(pivot=pivot, R_ave=self.R_ave, RT_ave=RT_ave)
# Initial chi-squared (or SSE) value.
chi2_sum = 0.0
@@ -890,10 +892,11 @@
# Unpack the parameters.
if self.pivot_opt:
- self._param_pivot = params[:3]
+ pivot = outer(self.spin_ones_struct, params[:3])
self._translation_vector = params[3:6]
ave_pos_beta, ave_pos_gamma, axis_theta, axis_phi, cone_s1 =
params[6:]
else:
+ pivot = self.pivot
self._translation_vector = params[:3]
ave_pos_beta, ave_pos_gamma, axis_theta, axis_phi, cone_s1 =
params[3:]
@@ -921,7 +924,7 @@
# Pre-calculate all the necessary vectors.
if self.pcs_flag:
- self.calc_vectors(self._param_pivot, self.R_ave, RT_ave)
+ self.calc_vectors(pivot=pivot, R_ave=self.R_ave, RT_ave=RT_ave)
# Initial chi-squared (or SSE) value.
chi2_sum = 0.0
@@ -1057,10 +1060,11 @@
# Unpack the parameters.
if self.pivot_opt:
- self._param_pivot = params[:3]
+ pivot = outer(self.spin_ones_struct, params[:3])
self._translation_vector = params[3:6]
ave_pos_alpha, ave_pos_beta, ave_pos_gamma, axis_theta, axis_phi,
cone_theta = params[6:]
else:
+ pivot = self.pivot
self._translation_vector = params[:3]
ave_pos_alpha, ave_pos_beta, ave_pos_gamma, axis_theta, axis_phi,
cone_theta = params[3:]
@@ -1085,7 +1089,7 @@
# Pre-calculate all the necessary vectors.
if self.pcs_flag:
- self.calc_vectors(self._param_pivot, self.R_ave, RT_ave)
+ self.calc_vectors(pivot=pivot, R_ave=self.R_ave, RT_ave=RT_ave)
# Initial chi-squared (or SSE) value.
chi2_sum = 0.0
@@ -1218,10 +1222,11 @@
# Unpack the parameters.
if self.pivot_opt:
- self._param_pivot = params[:3]
+ pivot = outer(self.spin_ones_struct, params[:3])
self._translation_vector = params[3:6]
ave_pos_alpha, ave_pos_beta, ave_pos_gamma, eigen_alpha,
eigen_beta, eigen_gamma, cone_theta_x, cone_theta_y, cone_sigma_max = params[6:]
else:
+ pivot = self.pivot
self._translation_vector = params[:3]
ave_pos_alpha, ave_pos_beta, ave_pos_gamma, eigen_alpha,
eigen_beta, eigen_gamma, cone_theta_x, cone_theta_y, cone_sigma_max = params[3:]
@@ -1243,7 +1248,7 @@
# Pre-calculate all the necessary vectors.
if self.pcs_flag:
- self.calc_vectors(self._param_pivot, self.R_ave, RT_ave)
+ self.calc_vectors(pivot=pivot, R_ave=self.R_ave, RT_ave=RT_ave)
# Initial chi-squared (or SSE) value.
chi2_sum = 0.0
@@ -1376,12 +1381,13 @@
# Unpack the parameters.
if self.pivot_opt:
- self._param_pivot = params[:3]
+ pivot = outer(self.spin_ones_struct, params[:3])
self._translation_vector = params[3:6]
- ave_pos_alpha, ave_pos_beta, ave_pos_gamma, eigen_alpha,
eigen_beta, eigen_gamma, cone_theta_x, cone_theta_y = params[6:]
+ ave_pos_beta, ave_pos_gamma, eigen_alpha, eigen_beta, eigen_gamma,
cone_theta_x, cone_theta_y = params[6:]
else:
+ pivot = self.pivot
self._translation_vector = params[:3]
- ave_pos_alpha, ave_pos_beta, ave_pos_gamma, eigen_alpha,
eigen_beta, eigen_gamma, cone_theta_x, cone_theta_y = params[3:]
+ ave_pos_beta, ave_pos_gamma, eigen_alpha, eigen_beta, eigen_gamma,
cone_theta_x, cone_theta_y = params[3:]
# Average position rotation.
euler_to_R_zyz(eigen_alpha, eigen_beta, eigen_gamma, self.R_eigen)
@@ -1393,7 +1399,7 @@
frame_order_2nd =
compile_2nd_matrix_pseudo_ellipse_free_rotor(self.frame_order_2nd, Rx2_eigen,
cone_theta_x, cone_theta_y)
# Reduce and rotate the tensors.
- self.reduce_and_rot(ave_pos_alpha, ave_pos_beta, ave_pos_gamma,
frame_order_2nd)
+ self.reduce_and_rot(0.0, ave_pos_beta, ave_pos_gamma, frame_order_2nd)
# Pre-transpose matrices for faster calculations.
RT_eigen = transpose(self.R_eigen)
@@ -1401,7 +1407,7 @@
# Pre-calculate all the necessary vectors.
if self.pcs_flag:
- self.calc_vectors(self._param_pivot, self.R_ave, RT_ave)
+ self.calc_vectors(pivot=pivot, R_ave=self.R_ave, RT_ave=RT_ave)
# Initial chi-squared (or SSE) value.
chi2_sum = 0.0
@@ -1534,10 +1540,11 @@
# Unpack the parameters.
if self.pivot_opt:
- self._param_pivot = params[:3]
+ pivot = outer(self.spin_ones_struct, params[:3])
self._translation_vector = params[3:6]
ave_pos_alpha, ave_pos_beta, ave_pos_gamma, eigen_alpha,
eigen_beta, eigen_gamma, cone_theta_x, cone_theta_y = params[6:]
else:
+ pivot = self.pivot
self._translation_vector = params[:3]
ave_pos_alpha, ave_pos_beta, ave_pos_gamma, eigen_alpha,
eigen_beta, eigen_gamma, cone_theta_x, cone_theta_y = params[3:]
@@ -1559,7 +1566,7 @@
# Pre-calculate all the necessary vectors.
if self.pcs_flag:
- self.calc_vectors(self._param_pivot, self.R_ave, RT_ave)
+ self.calc_vectors(pivot=pivot, R_ave=self.R_ave, RT_ave=RT_ave)
# Initial chi-squared (or SSE) value.
chi2_sum = 0.0
@@ -1774,15 +1781,16 @@
# Unpack the parameters.
if self.pivot_opt:
- self._param_pivot = params[:3]
+ pivot = outer(self.spin_ones_struct, params[:3])
self._translation_vector = params[3:6]
- ave_pos_alpha, ave_pos_beta, ave_pos_gamma, axis_theta, axis_phi,
sigma_max = params[6:]
+ ave_pos_alpha, ave_pos_beta, ave_pos_gamma, axis_alpha, sigma_max
= params[6:]
else:
+ pivot = self.pivot
self._translation_vector = params[:3]
- ave_pos_alpha, ave_pos_beta, ave_pos_gamma, axis_theta, axis_phi,
sigma_max = params[3:]
-
- # Generate the cone axis from the spherical angles.
- spherical_to_cartesian([1.0, axis_theta, axis_phi], self.cone_axis)
+ ave_pos_alpha, ave_pos_beta, ave_pos_gamma, axis_alpha, sigma_max
= params[3:]
+
+ # Generate the rotor axis.
+ self.cone_axis = create_rotor_axis_alpha(alpha=axis_alpha,
pivot=pivot[0], point=self.com)
# Pre-calculate the eigenframe rotation matrix.
two_vect_to_R(self.z_axis, self.cone_axis, self.R_eigen)
@@ -1802,7 +1810,7 @@
# Pre-calculate all the necessary vectors.
if self.pcs_flag:
- self.calc_vectors(self._param_pivot, self.R_ave, RT_ave)
+ self.calc_vectors(pivot=pivot, R_ave=self.R_ave, RT_ave=RT_ave)
# Initial chi-squared (or SSE) value.
chi2_sum = 0.0
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