Author: bugman
Date: Wed Sep 24 09:57:17 2014
New Revision: 25991
URL: http://svn.gna.org/viewcvs/relax?rev=25991&view=rev
Log:
Fixes for the recent commit restorations for the SciPy quadratic integration.
The cdp.quad_int flag is now passed into the
specific_analyses.frame_order.optimisation
multiprocessor command objects which then pass it into the target function.
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=25991&r1=25990&r2=25991&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 24 09:57:17 2014
@@ -493,7 +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=sobol_max_points,
sobol_oversample=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, quad_int=cdp.quad_int)
# Add the slave command and memo to the processor queue.
processor.add_to_queue(command, memo)
@@ -590,7 +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=sobol_max_points,
sobol_oversample=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, quad_int=cdp.quad_int)
# 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=25991&r1=25990&r2=25991&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 24 09:57:17 2014
@@ -941,7 +941,7 @@
class Frame_order_grid_command(Slave_command):
"""Command class for relaxation dispersion optimisation on the slave
processor."""
- def __init__(self, points=None, scaling_matrix=None, sim_index=None,
model=None, param_vector=None, full_tensors=None, full_in_ref_frame=None,
rdcs=None, rdc_err=None, rdc_weight=None, rdc_vect=None, rdc_const=None,
pcs=None, pcs_err=None, pcs_weight=None, atomic_pos=None, temp=None,
frq=None, paramag_centre=None, com=None, ave_pos_pivot=None, pivot=None,
pivot_opt=None, sobol_max_points=None, sobol_oversample=None, verbosity=None):
+ def __init__(self, points=None, scaling_matrix=None, sim_index=None,
model=None, param_vector=None, full_tensors=None, full_in_ref_frame=None,
rdcs=None, rdc_err=None, rdc_weight=None, rdc_vect=None, rdc_const=None,
pcs=None, pcs_err=None, pcs_weight=None, atomic_pos=None, temp=None,
frq=None, paramag_centre=None, com=None, ave_pos_pivot=None, pivot=None,
pivot_opt=None, sobol_max_points=None, sobol_oversample=None, verbosity=None,
quad_int=False):
"""Initialise the base class, storing all the master data to be sent
to the slave processor.
This method is run on the master processor whereas the run() method
is run on the slave processor.
@@ -998,6 +998,8 @@
@type sobol_oversample: int
@keyword verbosity: The verbosity level. This is used by
the result command returned to the master for printouts.
@type verbosity: int
+ @keyword quad_int: A flag which if True will perform high
precision numerical integration via the scipy.integrate quad(), dblquad() and
tplquad() integration methods rather than the rough quasi-random numerical
integration.
+ @type quad_int: bool
"""
# Store the arguments.
@@ -1026,6 +1028,7 @@
self.sobol_max_points = sobol_max_points
self.sobol_oversample = sobol_oversample
self.verbosity = verbosity
+ self.quad_int = quad_int
def run(self, processor, completed):
@@ -1077,7 +1080,7 @@
class Frame_order_minimise_command(Slave_command):
"""Command class for relaxation dispersion optimisation on the slave
processor."""
- def __init__(self, min_algor=None, min_options=None, func_tol=None,
grad_tol=None, max_iterations=None, scaling_matrix=None, constraints=False,
sim_index=None, model=None, param_vector=None, full_tensors=None,
full_in_ref_frame=None, rdcs=None, rdc_err=None, rdc_weight=None,
rdc_vect=None, rdc_const=None, pcs=None, pcs_err=None, pcs_weight=None,
atomic_pos=None, temp=None, frq=None, paramag_centre=None, com=None,
ave_pos_pivot=None, pivot=None, pivot_opt=None, sobol_max_points=None,
sobol_oversample=None, verbosity=None):
+ def __init__(self, min_algor=None, min_options=None, func_tol=None,
grad_tol=None, max_iterations=None, scaling_matrix=None, constraints=False,
sim_index=None, model=None, param_vector=None, full_tensors=None,
full_in_ref_frame=None, rdcs=None, rdc_err=None, rdc_weight=None,
rdc_vect=None, rdc_const=None, pcs=None, pcs_err=None, pcs_weight=None,
atomic_pos=None, temp=None, frq=None, paramag_centre=None, com=None,
ave_pos_pivot=None, pivot=None, pivot_opt=None, sobol_max_points=None,
sobol_oversample=None, verbosity=None, quad_int=False):
"""Initialise the base class, storing all the master data to be sent
to the slave processor.
This method is run on the master processor whereas the run() method
is run on the slave processor.
@@ -1142,6 +1145,8 @@
@type sobol_oversample: int
@keyword scaling_matrix: The diagonal, square scaling matrix.
@type scaling_matrix: numpy diagonal matrix
+ @keyword quad_int: A flag which if True will perform high
precision numerical integration via the scipy.integrate quad(), dblquad() and
tplquad() integration methods rather than the rough quasi-random numerical
integration.
+ @type quad_int: bool
"""
# Store some arguments.
@@ -1174,6 +1179,7 @@
self.sobol_max_points = sobol_max_points
self.sobol_oversample = sobol_oversample
self.verbosity = verbosity
+ self.quad_int = quad_int
# Linear constraints.
self.A, self.b = None, None
r25991 - in /branches/frame_order_cleanup/specific_analyses/frame_order: api.py optimisation.py