Author: bugman
Date: Wed Sep 17 17:11:41 2014
New Revision: 25879
URL: http://svn.gna.org/viewcvs/relax?rev=25879&view=rev
Log:
Fix for the rigid frame order model for the recent frame_order.sobol_setup
user function changes.
For this model, the number of Sobol' points normally is does not exist. This
is now correctly
handled.
Modified:
branches/frame_order_cleanup/specific_analyses/frame_order/api.py
branches/frame_order_cleanup/specific_analyses/frame_order/optimisation.py
Modified: branches/frame_order_cleanup/specific_analyses/frame_order/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/frame_order/api.py?rev=25879&r1=25878&r2=25879&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/frame_order/api.py
(original)
+++ branches/frame_order_cleanup/specific_analyses/frame_order/api.py Wed
Sep 17 17:11:41 2014
@@ -129,8 +129,14 @@
# Set up the data structures for the target function.
param_vector, full_tensors, full_in_ref_frame, rdcs, rdc_err,
rdc_weight, rdc_vect, rdc_const, pcs, pcs_err, pcs_weight, atomic_pos, temp,
frq, paramag_centre, com, ave_pos_pivot, pivot, pivot_opt =
target_fn_data_setup(sim_index=sim_index, verbosity=verbosity,
unset_fail=True)
+ # The Sobol' integration information.
+ sobol_max_points, sobol_oversample = None, None
+ if hasattr(cdp, 'sobol_max_points'):
+ sobol_max_points = cdp.sobol_max_points
+ sobol_oversample = cdp.sobol_oversample
+
# Set up the optimisation target function class.
- target_fn = frame_order.Frame_order(model=cdp.model,
init_params=param_vector, full_tensors=full_tensors,
full_in_ref_frame=full_in_ref_frame, rdcs=rdcs, rdc_errors=rdc_err,
rdc_weights=rdc_weight, rdc_vect=rdc_vect, dip_const=rdc_const, pcs=pcs,
pcs_errors=pcs_err, pcs_weights=pcs_weight, atomic_pos=atomic_pos, temp=temp,
frq=frq, paramag_centre=paramag_centre, scaling_matrix=scaling_matrix[0],
com=com, ave_pos_pivot=ave_pos_pivot, pivot=pivot, pivot_opt=pivot_opt,
sobol_max_points=cdp.sobol_max_points, sobol_oversample=cdp.sobol_oversample)
+ target_fn = frame_order.Frame_order(model=cdp.model,
init_params=param_vector, full_tensors=full_tensors,
full_in_ref_frame=full_in_ref_frame, rdcs=rdcs, rdc_errors=rdc_err,
rdc_weights=rdc_weight, rdc_vect=rdc_vect, dip_const=rdc_const, pcs=pcs,
pcs_errors=pcs_err, pcs_weights=pcs_weight, atomic_pos=atomic_pos, temp=temp,
frq=frq, paramag_centre=paramag_centre, scaling_matrix=scaling_matrix[0],
com=com, ave_pos_pivot=ave_pos_pivot, pivot=pivot, pivot_opt=pivot_opt,
sobol_max_points=sobol_max_points, sobol_oversample=sobol_oversample)
# Make a single function call. This will cause back calculation and
the data will be stored in the class instance.
chi2 = target_fn.func(param_vector)
@@ -459,6 +465,12 @@
warn(RelaxWarning("The '%s' model parameters are not
constrained, turning the linear constraint algorithm off." % cdp.model))
constraints = False
+ # The Sobol' integration information.
+ sobol_max_points, sobol_oversample = None, None
+ if hasattr(cdp, 'sobol_max_points'):
+ sobol_max_points = cdp.sobol_max_points
+ sobol_oversample = cdp.sobol_oversample
+
# Set up the data structures for the target function.
param_vector, full_tensors, full_in_ref_frame, rdcs, rdc_err,
rdc_weight, rdc_vect, rdc_const, pcs, pcs_err, pcs_weight, atomic_pos, temp,
frq, paramag_centre, com, ave_pos_pivot, pivot, pivot_opt =
target_fn_data_setup(sim_index=sim_index, verbosity=verbosity)
@@ -481,7 +493,7 @@
memo = Frame_order_memo(sim_index=sim_index,
scaling_matrix=scaling_matrix[0])
# Set up the command object to send to the slave and execute.
- command = Frame_order_grid_command(points=subdivision,
scaling_matrix=scaling_matrix[0], sim_index=sim_index, model=cdp.model,
param_vector=param_vector, full_tensors=full_tensors,
full_in_ref_frame=full_in_ref_frame, rdcs=rdcs, rdc_err=rdc_err,
rdc_weight=rdc_weight, rdc_vect=rdc_vect, rdc_const=rdc_const, pcs=pcs,
pcs_err=pcs_err, pcs_weight=pcs_weight, atomic_pos=atomic_pos, temp=temp,
frq=frq, paramag_centre=paramag_centre, com=com, ave_pos_pivot=ave_pos_pivot,
pivot=pivot, pivot_opt=pivot_opt, sobol_max_points=cdp.sobol_max_points,
sobol_oversample=cdp.sobol_oversample, verbosity=verbosity)
+ command = Frame_order_grid_command(points=subdivision,
scaling_matrix=scaling_matrix[0], sim_index=sim_index, model=cdp.model,
param_vector=param_vector, full_tensors=full_tensors,
full_in_ref_frame=full_in_ref_frame, rdcs=rdcs, rdc_err=rdc_err,
rdc_weight=rdc_weight, rdc_vect=rdc_vect, rdc_const=rdc_const, pcs=pcs,
pcs_err=pcs_err, pcs_weight=pcs_weight, atomic_pos=atomic_pos, temp=temp,
frq=frq, paramag_centre=paramag_centre, com=com, ave_pos_pivot=ave_pos_pivot,
pivot=pivot, pivot_opt=pivot_opt, sobol_max_points=sobol_max_points,
sobol_oversample=sobol_oversample, verbosity=verbosity)
# Add the slave command and memo to the processor queue.
processor.add_to_queue(command, memo)
@@ -564,6 +576,12 @@
# Set up the data structures for the target function.
param_vector, full_tensors, full_in_ref_frame, rdcs, rdc_err,
rdc_weight, rdc_vect, rdc_const, pcs, pcs_err, pcs_weight, atomic_pos, temp,
frq, paramag_centre, com, ave_pos_pivot, pivot, pivot_opt =
target_fn_data_setup(sim_index=sim_index, verbosity=verbosity,
unset_fail=True)
+ # The Sobol' integration information.
+ sobol_max_points, sobol_oversample = None, None
+ if hasattr(cdp, 'sobol_max_points'):
+ sobol_max_points = cdp.sobol_max_points
+ sobol_oversample = cdp.sobol_oversample
+
# Get the Processor box singleton (it contains the Processor
instance) and alias the Processor.
processor_box = Processor_box()
processor = processor_box.processor
@@ -572,7 +590,7 @@
memo = Frame_order_memo(sim_index=sim_index,
scaling_matrix=scaling_matrix[0])
# Set up the command object to send to the slave and execute.
- command = Frame_order_minimise_command(min_algor=min_algor,
min_options=min_options, func_tol=func_tol, grad_tol=grad_tol,
max_iterations=max_iterations, scaling_matrix=scaling_matrix[0],
constraints=constraints, sim_index=sim_index, model=cdp.model,
param_vector=param_vector, full_tensors=full_tensors,
full_in_ref_frame=full_in_ref_frame, rdcs=rdcs, rdc_err=rdc_err,
rdc_weight=rdc_weight, rdc_vect=rdc_vect, rdc_const=rdc_const, pcs=pcs,
pcs_err=pcs_err, pcs_weight=pcs_weight, atomic_pos=atomic_pos, temp=temp,
frq=frq, paramag_centre=paramag_centre, com=com, ave_pos_pivot=ave_pos_pivot,
pivot=pivot, pivot_opt=pivot_opt, sobol_max_points=cdp.sobol_max_points,
sobol_oversample=cdp.sobol_oversample, verbosity=verbosity)
+ command = Frame_order_minimise_command(min_algor=min_algor,
min_options=min_options, func_tol=func_tol, grad_tol=grad_tol,
max_iterations=max_iterations, scaling_matrix=scaling_matrix[0],
constraints=constraints, sim_index=sim_index, model=cdp.model,
param_vector=param_vector, full_tensors=full_tensors,
full_in_ref_frame=full_in_ref_frame, rdcs=rdcs, rdc_err=rdc_err,
rdc_weight=rdc_weight, rdc_vect=rdc_vect, rdc_const=rdc_const, pcs=pcs,
pcs_err=pcs_err, pcs_weight=pcs_weight, atomic_pos=atomic_pos, temp=temp,
frq=frq, paramag_centre=paramag_centre, com=com, ave_pos_pivot=ave_pos_pivot,
pivot=pivot, pivot_opt=pivot_opt, sobol_max_points=sobol_max_points,
sobol_oversample=sobol_oversample, verbosity=verbosity)
# Add the slave command and memo to the processor queue.
processor.add_to_queue(command, memo)
Modified:
branches/frame_order_cleanup/specific_analyses/frame_order/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/frame_order/optimisation.py?rev=25879&r1=25878&r2=25879&view=diff
==============================================================================
---
branches/frame_order_cleanup/specific_analyses/frame_order/optimisation.py
(original)
+++
branches/frame_order_cleanup/specific_analyses/frame_order/optimisation.py
Wed Sep 17 17:11:41 2014
@@ -83,8 +83,14 @@
# Set up the data structures for the target function.
param_vector, full_tensors, full_in_ref_frame, rdcs, rdc_err,
rdc_weight, rdc_vect, rdc_const, pcs, pcs_err, pcs_weight, atomic_pos, temp,
frq, paramag_centre, com, ave_pos_pivot, pivot, pivot_opt =
target_fn_data_setup(verbosity=0, unset_fail=True)
+ # The Sobol' integration information.
+ sobol_max_points, sobol_oversample = None, None
+ if hasattr(cdp, 'sobol_max_points'):
+ sobol_max_points = cdp.sobol_max_points
+ sobol_oversample = cdp.sobol_oversample
+
# Set up the optimisation target function class.
- target_fn = Frame_order(model=cdp.model, init_params=param_vector,
full_tensors=full_tensors, full_in_ref_frame=full_in_ref_frame, rdcs=rdcs,
rdc_errors=rdc_err, rdc_weights=rdc_weight, rdc_vect=rdc_vect,
dip_const=rdc_const, pcs=pcs, pcs_errors=pcs_err, pcs_weights=pcs_weight,
atomic_pos=atomic_pos, temp=temp, frq=frq, paramag_centre=paramag_centre,
scaling_matrix=None, com=com, ave_pos_pivot=ave_pos_pivot, pivot=pivot,
pivot_opt=pivot_opt, sobol_max_points=cdp.sobol_max_points,
sobol_oversample=cdp.sobol_oversample)
+ target_fn = Frame_order(model=cdp.model, init_params=param_vector,
full_tensors=full_tensors, full_in_ref_frame=full_in_ref_frame, rdcs=rdcs,
rdc_errors=rdc_err, rdc_weights=rdc_weight, rdc_vect=rdc_vect,
dip_const=rdc_const, pcs=pcs, pcs_errors=pcs_err, pcs_weights=pcs_weight,
atomic_pos=atomic_pos, temp=temp, frq=frq, paramag_centre=paramag_centre,
scaling_matrix=None, com=com, ave_pos_pivot=ave_pos_pivot, pivot=pivot,
pivot_opt=pivot_opt, sobol_max_points=sobol_max_points,
sobol_oversample=sobol_oversample)
# The Sobol' sequence dimensions.
if cdp.model in [MODEL_ISO_CONE, MODEL_ISO_CONE_FREE_ROTOR,
MODEL_PSEUDO_ELLIPSE, MODEL_PSEUDO_ELLIPSE_FREE_ROTOR]:
r25879 - in /branches/frame_order_cleanup/specific_analyses/frame_order: api.py optimisation.py