Author: bugman
Date: Mon Oct 20 11:52:52 2014
New Revision: 26314
URL: http://svn.gna.org/viewcvs/relax?rev=26314&view=rev
Log:
The splitting of the rigid model grid search into rotation and translation
parts is now optional.
In the frame order auto-analysis, the rigid_grid_split argument has been
introduced. The
alternating algorithm of performing a grid search over the rotational space
followed by translation
is now optional and turned off by default. The reason is because the global
minimum is sometimes
missed with this shortcut algorithm.
Modified:
branches/frame_order_cleanup/auto_analyses/frame_order.py
Modified: branches/frame_order_cleanup/auto_analyses/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/auto_analyses/frame_order.py?rev=26314&r1=26313&r2=26314&view=diff
==============================================================================
--- branches/frame_order_cleanup/auto_analyses/frame_order.py (original)
+++ branches/frame_order_cleanup/auto_analyses/frame_order.py Mon Oct 20
11:52:52 2014
@@ -369,7 +369,7 @@
# Debugging and test suite variables.
_final_state = True
- def __init__(self, data_pipe_full=None, data_pipe_subset=None,
pipe_bundle=None, results_dir=None, pre_run_dir=None, opt_rigid=None,
opt_subset=None, opt_full=None, opt_mc=None, mc_sim_num=500,
models=MODEL_LIST_NONREDUNDANT, brownian_step_size=2.0, brownian_snapshot=10,
brownian_total=1000):
+ def __init__(self, data_pipe_full=None, data_pipe_subset=None,
pipe_bundle=None, results_dir=None, pre_run_dir=None, opt_rigid=None,
opt_subset=None, opt_full=None, opt_mc=None, mc_sim_num=500,
models=MODEL_LIST_NONREDUNDANT, brownian_step_size=2.0, brownian_snapshot=10,
brownian_total=1000, rigid_grid_split=False):
"""Perform the full frame order analysis.
@param data_pipe_full: The name of the data pipe containing
all of the RDC and PCS data.
@@ -400,6 +400,8 @@
@type brownian_snapshot: int
@keyword brownian_total: The total argument for the
pseudo-Brownian dynamics simulation frame_order.simulate user function.
@type brownian_total: int
+ @keyword rigid_grid_split: A flag which if True will cause the
grid search for the rigid model to be split so that the rotation is optimised
first followed by the translation. When combined with grid zooming, this can
save optimisation time. However it may result in the global minimum being
missed.
+ @type rigid_grid_split: bool
"""
# Execution lock.
@@ -422,6 +424,7 @@
self.brownian_step_size = brownian_step_size
self.brownian_snapshot = brownian_snapshot
self.brownian_total = brownian_total
+ self.rigid_grid_split = rigid_grid_split
# Re-order the models to enable the parameter nesting protocol.
self.models = self.reorder_models(models)
@@ -1098,29 +1101,49 @@
# Optimisation.
opt = self.opt_rigid
if opt != None:
- # Split zooming grid search for the translation.
- print("\n\nTranslation active - splitting the grid search and
iterating.")
- self.interpreter.value.set(param='ave_pos_x', val=0.0)
- self.interpreter.value.set(param='ave_pos_y', val=0.0)
- self.interpreter.value.set(param='ave_pos_z', val=0.0)
- for i in opt.loop_grid():
- # Set the zooming grid search level.
- zoom = opt.get_grid_zoom_level(i)
- if zoom != None:
- self.interpreter.minimise.grid_zoom(level=zoom)
-
- # The numerical optimisation settings.
- self.interpreter.frame_order.quad_int(opt.get_grid_quad_int(i))
- self.sobol_setup(opt.get_grid_sobol_info(i))
-
- # The number of increments.
- inc = opt.get_grid_inc(i)
-
- # First optimise the rotation.
- self.interpreter.minimise.grid_search(inc=[None, None, None,
inc, inc, inc], skip_preset=False)
-
- # Then the translation.
- self.interpreter.minimise.grid_search(inc=[inc, inc, inc,
None, None, None], skip_preset=False)
+ # Grid search alternation.
+ if self.rigid_grid_split:
+ # Split zooming grid search for the translation.
+ print("\n\nTranslation active - splitting the grid search and
iterating.")
+ self.interpreter.value.set(param='ave_pos_x', val=0.0)
+ self.interpreter.value.set(param='ave_pos_y', val=0.0)
+ self.interpreter.value.set(param='ave_pos_z', val=0.0)
+ for i in opt.loop_grid():
+ # Set the zooming grid search level.
+ zoom = opt.get_grid_zoom_level(i)
+ if zoom != None:
+ self.interpreter.minimise.grid_zoom(level=zoom)
+
+ # The numerical optimisation settings.
+
self.interpreter.frame_order.quad_int(opt.get_grid_quad_int(i))
+ self.sobol_setup(opt.get_grid_sobol_info(i))
+
+ # The number of increments.
+ inc = opt.get_grid_inc(i)
+
+ # First optimise the rotation.
+ self.interpreter.minimise.grid_search(inc=[None, None,
None, inc, inc, inc], skip_preset=False)
+
+ # Then the translation.
+ self.interpreter.minimise.grid_search(inc=[inc, inc, inc,
None, None, None], skip_preset=False)
+
+ # Normal grid search.
+ else:
+ for i in opt.loop_grid():
+ # Set the zooming grid search level.
+ zoom = opt.get_grid_zoom_level(i)
+ if zoom != None:
+ self.interpreter.minimise.grid_zoom(level=zoom)
+
+ # The numerical optimisation settings.
+
self.interpreter.frame_order.quad_int(opt.get_grid_quad_int(i))
+ self.sobol_setup(opt.get_grid_sobol_info(i))
+
+ # The number of increments.
+ inc = opt.get_grid_inc(i)
+
+ # Grid search
+ self.interpreter.minimise.grid_search(inc=inc,
skip_preset=False)
# Minimise.
for i in opt.loop_min():
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