Author: bugman
Date: Fri Oct 2 12:15:57 2015
New Revision: 27945
URL: http://svn.gna.org/viewcvs/relax?rev=27945&view=rev
Log:
Merged revisions 24715-24717 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_cleanup
........
r24715 | bugman | 2014-07-24 16:47:36 +0200 (Thu, 24 Jul 2014) | 5 lines
Turned on the optimisation in the Frame_order.test_cam_rigid system test.
This is to catch a number of failures in the frame order grid search.
........
r24716 | bugman | 2014-07-24 16:50:44 +0200 (Thu, 24 Jul 2014) | 5 lines
Activated the grid search in the frame order system tests using the CaM
synthetic data.
This is set to one increment so that the tests can complete in a reasonable
time.
........
r24717 | bugman | 2014-07-24 16:53:06 +0200 (Thu, 24 Jul 2014) | 6 lines
Fix for the specific_analyses.frame_order.optimisation.grid_row() function.
This can now handle the case of a single grid increment. The change is
similar to r163 in the minfx
project (https://mail.gna.org/public/minfx-commits/2014-07/msg00015.html).
........
Modified:
trunk/ (props changed)
trunk/specific_analyses/frame_order/optimisation.py
trunk/test_suite/system_tests/frame_order.py
trunk/test_suite/system_tests/scripts/frame_order/cam/base_script.py
Propchange: trunk/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Fri Oct 2 12:15:57 2015
@@ -1 +1 @@
-/branches/frame_order_cleanup:1-23195,23197-23205,23208-23646,23650-23673,23682-23709,23713-23783,23807-23812,23856-23887,23935-23983,23985-24322,24327-24346,24352-24411,24433-24509,24514-24520,24522-24524,24530-24539,24560-24667,24709-24713
+/branches/frame_order_cleanup:1-23195,23197-23205,23208-23646,23650-23673,23682-23709,23713-23783,23807-23812,23856-23887,23935-23983,23985-24322,24327-24346,24352-24411,24433-24509,24514-24520,24522-24524,24530-24539,24560-24667,24709-24713,24715-24717
Modified: trunk/specific_analyses/frame_order/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/optimisation.py?rev=27945&r1=27944&r2=27945&view=diff
==============================================================================
--- trunk/specific_analyses/frame_order/optimisation.py (original)
+++ trunk/specific_analyses/frame_order/optimisation.py Fri Oct 2 12:15:57
2015
@@ -73,24 +73,33 @@
# Linear grid.
if dist_type == None:
+ # Handle a single increment.
+ if incs == 1:
+ row.append((lower + upper) / 2.0)
+
# Loop over the increments.
- for i in range(incs):
- # The row.
- row.append(lower + i * (upper - lower) / (incs - 1.0))
+ else:
+ for i in range(incs):
+ row.append(lower + i * (upper - lower) / (incs - 1.0))
# Inverse cos distribution.
elif dist_type == 'acos':
+ # Handle a single increment.
+ if incs == 1:
+ row.append((lower + upper) / 2.0)
+
# Generate the increment values of v from cos(upper) to cos(lower).
- v = zeros(incs, float64)
- val = (cos(lower) - cos(upper)) / (incs - 1.0)
- for i in range(incs):
- v[-i-1] = cos(upper) + float(i) * val
-
- # Generate the distribution.
- row = arccos(v)
+ else:
+ v = zeros(incs, float64)
+ val = (cos(lower) - cos(upper)) / (incs - 1.0)
+ for i in range(incs):
+ v[-i-1] = cos(upper) + float(i) * val
+
+ # Generate the distribution.
+ row = arccos(v)
# Remove the last point.
- if not end_point:
+ if incs != 1 and not end_point:
row = row[:-1]
# Return the row (as a list).
Modified: trunk/test_suite/system_tests/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/frame_order.py?rev=27945&r1=27944&r2=27945&view=diff
==============================================================================
--- trunk/test_suite/system_tests/frame_order.py (original)
+++ trunk/test_suite/system_tests/frame_order.py Fri Oct 2 12:15:57
2015
@@ -575,7 +575,7 @@
"""Test the rigid frame order model of CaM."""
# The flags, execute the script, and then check the chi2 value.
- self.flags()
+ self.flags(opt=True)
self.interpreter.run(script_file=self.cam_path+'rigid.py')
self.check_chi2(0.081171019382935666)
Modified: trunk/test_suite/system_tests/scripts/frame_order/cam/base_script.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/frame_order/cam/base_script.py?rev=27945&r1=27944&r2=27945&view=diff
==============================================================================
--- trunk/test_suite/system_tests/scripts/frame_order/cam/base_script.py
(original)
+++ trunk/test_suite/system_tests/scripts/frame_order/cam/base_script.py
Fri Oct 2 12:15:57 2015
@@ -196,8 +196,8 @@
# Optimise.
if hasattr(status, 'flag_opt') and status.flag_opt:
- #self._execute_uf(uf_name='grid_search', inc=11)
- self._execute_uf(uf_name='minimise', min_algor='simplex',
constraints=True, max_iter=1)
+ self._execute_uf(uf_name='minimise.grid_search', inc=1)
+ self._execute_uf(uf_name='minimise.execute',
min_algor='simplex', constraints=True, max_iter=1)
# Test Monte Carlo simulations.
self._execute_uf(uf_name='monte_carlo.setup', number=3)
r27945 - in /trunk: ./ specific_analyses/frame_order/ test_suite/system_tests/ test_suite/system_tests/scripts/frame_order/cam/