Author: bugman
Date: Wed Feb 1 13:28:57 2012
New Revision: 15286
URL: http://svn.gna.org/viewcvs/relax?rev=15286&view=rev
Log:
Started to convert the frame order rotor model to quasi-random numerical
integration.
Modified:
branches/frame_order_testing/maths_fns/frame_order.py
Modified: branches/frame_order_testing/maths_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/maths_fns/frame_order.py?rev=15286&r1=15285&r2=15286&view=diff
==============================================================================
--- branches/frame_order_testing/maths_fns/frame_order.py (original)
+++ branches/frame_order_testing/maths_fns/frame_order.py Wed Feb 1 13:28:57
2012
@@ -36,7 +36,7 @@
from maths_fns.alignment_tensor import to_5D, to_tensor
from maths_fns.chi2 import chi2
from maths_fns.coord_transform import spherical_to_cartesian
-from maths_fns.frame_order_matrix_ops import compile_2nd_matrix_free_rotor,
compile_2nd_matrix_iso_cone, compile_2nd_matrix_iso_cone_free_rotor,
compile_2nd_matrix_iso_cone_torsionless, compile_2nd_matrix_pseudo_ellipse,
compile_2nd_matrix_pseudo_ellipse_free_rotor,
compile_2nd_matrix_pseudo_ellipse_torsionless, compile_2nd_matrix_rotor,
reduce_alignment_tensor, pcs_numeric_int_iso_cone,
pcs_numeric_int_iso_cone_mcint, pcs_numeric_int_iso_cone_torsionless,
pcs_numeric_int_iso_cone_torsionless_mcint, pcs_numeric_int_pseudo_ellipse,
pcs_numeric_int_pseudo_ellipse_qrint,
pcs_numeric_int_pseudo_ellipse_torsionless,
pcs_numeric_int_pseudo_ellipse_torsionless_mcint, pcs_numeric_int_rotor,
pcs_numeric_int_rotor_mcint
+from maths_fns.frame_order_matrix_ops import compile_2nd_matrix_free_rotor,
compile_2nd_matrix_iso_cone, compile_2nd_matrix_iso_cone_free_rotor,
compile_2nd_matrix_iso_cone_torsionless, compile_2nd_matrix_pseudo_ellipse,
compile_2nd_matrix_pseudo_ellipse_free_rotor,
compile_2nd_matrix_pseudo_ellipse_torsionless, compile_2nd_matrix_rotor,
reduce_alignment_tensor, pcs_numeric_int_iso_cone,
pcs_numeric_int_iso_cone_mcint, pcs_numeric_int_iso_cone_torsionless,
pcs_numeric_int_iso_cone_torsionless_mcint, pcs_numeric_int_pseudo_ellipse,
pcs_numeric_int_pseudo_ellipse_qrint,
pcs_numeric_int_pseudo_ellipse_torsionless,
pcs_numeric_int_pseudo_ellipse_torsionless_mcint, pcs_numeric_int_rotor,
pcs_numeric_int_rotor_qrint
from maths_fns.kronecker_product import kron_prod
from maths_fns import order_parameters
from maths_fns.rotation_matrix import euler_to_R_zyz
@@ -270,13 +270,10 @@
self.drdc_theta = zeros((self.total_num_params, self.num_align,
self.num_rdc), float64)
self.d2rdc_theta = zeros((self.total_num_params,
self.total_num_params, self.num_align, self.num_rdc), float64)
- # The Sobol' sequence data.
- if mcint:
- self.create_sobol_data(m=3, n=200000)
-
- # The target function aliases (Monte Carlo integration).
+ # The Sobol' sequence data and target function aliases (quasi-random
integration).
if mcint:
if model == 'pseudo-ellipse':
+ self.create_sobol_data(m=3, n=self.num_int_pts)
self.func = self.func_pseudo_ellipse_qrint
elif model == 'pseudo-ellipse, torsionless':
self.func = self.func_pseudo_ellipse_torsionless_mcint
@@ -295,7 +292,8 @@
elif model == 'line, free rotor':
self.func = self.func_line_free_rotor_mcint
elif model == 'rotor':
- self.func = self.func_rotor_mcint
+ self.create_sobol_data(m=1, n=self.num_int_pts)
+ self.func = self.func_rotor_qrint
elif model == 'rigid':
self.func = self.func_rigid
elif model == 'free rotor':
@@ -507,7 +505,7 @@
# PCS via Monte Carlo integration.
if self.pcs_flag:
# Numerical integration of the PCSs.
- pcs_numeric_int_rotor_mcint(N=self.num_int_pts, sigma_max=pi,
c=self.pcs_const, full_in_ref_frame=self.full_in_ref_frame,
r_pivot_atom=self.r_pivot_atom, r_pivot_atom_rev=self.r_pivot_atom_rev,
r_ln_pivot=self.r_ln_pivot, A=self.A_3D, R_eigen=self.R_eigen,
RT_eigen=RT_eigen, Ri_prime=self.Ri_prime, pcs_theta=self.pcs_theta,
pcs_theta_err=self.pcs_theta_err, missing_pcs=self.missing_pcs,
error_flag=False)
+ pcs_numeric_int_rotor_qrint(N=self.num_int_pts, sigma_max=pi,
c=self.pcs_const, full_in_ref_frame=self.full_in_ref_frame,
r_pivot_atom=self.r_pivot_atom, r_pivot_atom_rev=self.r_pivot_atom_rev,
r_ln_pivot=self.r_ln_pivot, A=self.A_3D, R_eigen=self.R_eigen,
RT_eigen=RT_eigen, Ri_prime=self.Ri_prime, pcs_theta=self.pcs_theta,
pcs_theta_err=self.pcs_theta_err, missing_pcs=self.missing_pcs,
error_flag=False)
# Calculate and sum the single alignment chi-squared value (for
the PCS).
for i in xrange(self.num_align):
@@ -1613,10 +1611,10 @@
return chi2_sum
- def func_rotor_mcint(self, params):
+ def func_rotor_qrint(self, params):
"""Target function for rotor model optimisation.
- This function optimises the isotropic cone model parameters using
the RDC and PCS base data. Simple Monte Carlo integration is used for the
PCS.
+ This function optimises the isotropic cone model parameters using
the RDC and PCS base data. Quasi-random, Sobol' sequence based, numerical
integration is used for the PCS.
@param params: The vector of parameter values. These are the
tensor rotation angles {alpha, beta, gamma, theta, phi, sigma_max}.
@@ -1678,7 +1676,7 @@
# PCS via Monte Carlo integration.
if self.pcs_flag:
# Numerical integration of the PCSs.
- pcs_numeric_int_rotor_mcint(N=self.num_int_pts,
sigma_max=sigma_max, c=self.pcs_const,
full_in_ref_frame=self.full_in_ref_frame, r_pivot_atom=self.r_pivot_atom,
r_pivot_atom_rev=self.r_pivot_atom_rev, r_ln_pivot=self.r_ln_pivot,
A=self.A_3D, R_eigen=self.R_eigen, RT_eigen=RT_eigen, Ri_prime=self.Ri_prime,
pcs_theta=self.pcs_theta, pcs_theta_err=self.pcs_theta_err,
missing_pcs=self.missing_pcs, error_flag=False)
+ pcs_numeric_int_rotor_qrint(points=self.sobol_angles,
sigma_max=sigma_max, c=self.pcs_const,
full_in_ref_frame=self.full_in_ref_frame, r_pivot_atom=self.r_pivot_atom,
r_pivot_atom_rev=self.r_pivot_atom_rev, r_ln_pivot=self.r_ln_pivot,
A=self.A_3D, R_eigen=self.R_eigen, RT_eigen=RT_eigen, Ri_prime=self.Ri_prime,
pcs_theta=self.pcs_theta, pcs_theta_err=self.pcs_theta_err,
missing_pcs=self.missing_pcs, error_flag=False)
# Calculate and sum the single alignment chi-squared value (for
the PCS).
for i in xrange(self.num_align):
r15286 - /branches/frame_order_testing/maths_fns/frame_order.py