Author: bugman
Date: Fri Oct 2 14:06:02 2015
New Revision: 27953
URL: http://svn.gna.org/viewcvs/relax?rev=27953&view=rev
Log:
Merged revisions 25964,25970,25981,25983,25987-26010 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_cleanup
........
r25964 | bugman | 2014-09-23 10:19:40 +0200 (Tue, 23 Sep 2014) | 7 lines
Shifted the specific_analyses.frame_order.variables module into
lib.frame_order.
This is both to minimise circular dependencies, as previously the
specific_analyses.frame_order
modules import from target_functions.frame_order and vice-versa, and to
allow the relax library
functions to have access to these variables.
........
r25970 | bugman | 2014-09-23 17:13:58 +0200 (Tue, 23 Sep 2014) | 9 lines
Implemented the frame_order.simulate user function backend for the double
rotor frame order model.
This involved extending the algorithm to loop over N states, where N=2 for
the double rotor and N=1
for all other models. To handle the rotations being about the x and
y-axes, an axis permutation
algorithm is used to shift these axes to z prior to decomposing to the
torsion-tilt angles. The
reverse permutation is used to shift the axes back after correcting for
being outside of the allowed
angles.
........
r25981 | bugman | 2014-09-23 20:05:55 +0200 (Tue, 23 Sep 2014) | 6 lines
Fixes for the specific_analyses.frame_order.geometric.average_position()
function.
The recent trunk changes with the structural object Internal_selection
class required a change in
this function.
........
r25983 | bugman | 2014-09-23 20:09:49 +0200 (Tue, 23 Sep 2014) | 6 lines
Updated the lib.frame_order.simulation.brownian() function.
This now uses the internal structural object selection object logic - the
selection() method is
called to obtain the Internal_selection object, and this is then passed
into the rotation() method.
........
r25987 | bugman | 2014-09-24 09:31:51 +0200 (Wed, 24 Sep 2014) | 26 lines
Reverted r23202.
The command used was:
svn merge -r23202:23201 .
This is part of restoring the SciPy quadratic integration in the frame
order target functions.
Although incredibly slow, this will be useful for refining the final
results, especially for models
whereby the number of Sobol' points collapses to zero.
.....
r23202 | bugman | 2014-05-16 14:31:11 +0200 (Fri, 16 May 2014) | 6 lines
Changed paths:
M /branches/frame_order_cleanup/lib/frame_order/iso_cone.py
M /branches/frame_order_cleanup/lib/frame_order/iso_cone_torsionless.py
M /branches/frame_order_cleanup/lib/frame_order/matrix_ops.py
M /branches/frame_order_cleanup/lib/frame_order/pseudo_ellipse.py
M
/branches/frame_order_cleanup/lib/frame_order/pseudo_ellipse_torsionless.py
M /branches/frame_order_cleanup/lib/frame_order/rotor.py
Deletion of all of the Scipy quadratic integration functions for the PCS
in the relax library.
These are no longer used, as they are far too slow. The quasi-random
functions have long replaced
these.
.....
........
r25988 | bugman | 2014-09-24 09:33:25 +0200 (Wed, 24 Sep 2014) | 20 lines
Reverted r23200.
The command used was:
svn merge -r23200:23199 .
This is part of restoring the SciPy quadratic integration in the frame
order target functions.
Although incredibly slow, this will be useful for refining the final
results, especially for models
whereby the number of Sobol' points collapses to zero.
.....
r23200 | bugman | 2014-05-16 14:14:48 +0200 (Fri, 16 May 2014) | 5 lines
Changed paths:
M /branches/frame_order_cleanup/target_functions/frame_order.py
Import cleanup for the frame order target functions.
The Scipy quadratic integration functions for the PCS have been removed.
.....
........
r25989 | bugman | 2014-09-24 09:43:32 +0200 (Wed, 24 Sep 2014) | 22 lines
Reverted r23199.
The command used was:
svn merge -r23199:23198 .
This is part of restoring the SciPy quadratic integration in the frame
order target functions.
Although incredibly slow, this will be useful for refining the final
results, especially for models
whereby the number of Sobol' points collapses to zero.
.....
r23199 | bugman | 2014-05-16 14:12:07 +0200 (Fri, 16 May 2014) | 7 lines
Changed paths:
M /branches/frame_order_cleanup/target_functions/frame_order.py
Deletion of half of the frame order target functions.
All of the target functions using Scipy quadratic integration (which
cause a frame order analysis to
take over 1,000,000 years to complete) have been deleted. The
quasi-random target functions that
replace these have been renamed to remove the '_qrint' ending.
.....
........
r25990 | bugman | 2014-09-24 09:52:57 +0200 (Wed, 24 Sep 2014) | 42 lines
Reverted r23309, the deletion of the frame_order.quad_int user function and
the rest of the backend.
The command used was:
svn merge -r23309:23308 .
This is part of restoring the SciPy quadratic integration in the frame
order target functions.
Although incredibly slow, this will be useful for refining the final
results, especially for models
whereby the number of Sobol' points collapses to zero.
.....
r23309 | bugman | 2014-05-21 17:06:17 +0200 (Wed, 21 May 2014) | 4 lines
Changed paths:
M /branches/frame_order_cleanup/auto_analyses/frame_order.py
M
/branches/frame_order_cleanup/specific_analyses/frame_order/optimisation.py
M /branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
M /branches/frame_order_cleanup/target_functions/frame_order.py
M
/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor/frame_order.py
M
/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order.py
M
/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order.py
M
/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone/frame_order.py
M
/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.py
M
/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order.py
M
/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/frame_order.py
M
/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order.py
M
/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse/multi_processor_test.py
M
/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order.py
M
/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order.py
M
/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.py
M
/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/frame_order.py
M
/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor/frame_order.py
M
/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor2/frame_order.py
M
/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor2/pcs_only/frame_order.py
M
/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor_2_state/frame_order.py
M /branches/frame_order_cleanup/user_functions/frame_order.py
Deletion of the frame_order.quad_int user function.
This no longer has a purpose, as the incredibly slow quadratic
integration code has been removed
from relax.
.....
........
r25991 | bugman | 2014-09-24 09:57:17 +0200 (Wed, 24 Sep 2014) | 6 lines
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.
........
r25992 | bugman | 2014-09-24 10:01:07 +0200 (Wed, 24 Sep 2014) | 5 lines
Removed the call to the frame_order.quad_int user function in the
auto-analysis.
This was the result of a bad restoring merger of an old commit.
........
r25993 | bugman | 2014-09-24 10:14:53 +0200 (Wed, 24 Sep 2014) | 5 lines
The quad_int argument for the frame order target function class now
defaults to False.
This is so that quasi-random Sobol' numerical integration will be used by
default.
........
r25994 | bugman | 2014-09-24 10:16:53 +0200 (Wed, 24 Sep 2014) | 5 lines
The cdp.quad_int flag is now passed into the target function for the frame
order calculate() method.
This is for the minimise.calculate user function backend.
........
r25995 | bugman | 2014-09-24 10:25:13 +0200 (Wed, 24 Sep 2014) | 7 lines
Fixes for the missing cdp.quad_int flag.
If the cdp.quad_int flag is missing, this is now set to False before
setting up the target function
class. The previous behaviour was that the frame_order.quad_int user
function must be called prior
to optimisation. Now it is optional for turning this flag on and off.
........
r25996 | bugman | 2014-09-24 10:26:09 +0200 (Wed, 24 Sep 2014) | 3 lines
Fix for r25994 - the cdp.quad_int flag was not passed into the target
function properly.
........
r25997 | bugman | 2014-09-24 10:29:31 +0200 (Wed, 24 Sep 2014) | 5 lines
The RDC only optimisation now defaults to the *_qrint() frame order target
functions.
This restores the earlier behaviour prior to the restoration of the SciPy
quadratic integration.
........
r25998 | bugman | 2014-09-24 10:53:03 +0200 (Wed, 24 Sep 2014) | 9 lines
Clean up for the frame order target function aliasing.
The Scipy quadratic integration and the quasi-random Sobol' integration
target functions are now
aliased using the getattr() Python method to programmatically choose one or
the other. The rigid
model has been removed from the list as it is not a numeric model, and the
func_double_rotor()
target function has been renamed to func_double_rotor_qrint() to make it
consistent with the naming
of the other target functions.
........
r25999 | bugman | 2014-09-24 11:22:28 +0200 (Wed, 24 Sep 2014) | 7 lines
Renaming of all the frame order target functions and PCS integration
functions.
For consistency, all quasi-random Sobol' integration functions now use the
'qr_int' tag whereas the
SciPy quadratic integration functions use the 'quad_int' tag. This is not
only in the target
function names but also the PCS integration functions in lib.frame_order.
........
r26000 | bugman | 2014-09-24 11:38:12 +0200 (Wed, 24 Sep 2014) | 9 lines
Duplicated all Frame_order.test_cam_* system tests for testing the SciPy
quadratic integration.
The Frame_order.test_cam_* system tests have all been renamed to
Frame_order.test_cam_qr_int_*.
These have been duplicated and renamed to Frame_order.test_cam_quad_int_*.
The flag() system test
method has been extended to include the quad_int flag which is then stored
in the status object and
used in the base CaM frame order system test script to activate the
frame_order.quad_int user
function.
........
r26001 | bugman | 2014-09-24 13:17:16 +0200 (Wed, 24 Sep 2014) | 5 lines
Activated the quad_int flag for a number of the
Frame_order.test_cam_quad_int_* system tests.
The quad_int argument for the flags() test suite method had been missed for
a few of these tests.
........
r26002 | bugman | 2014-09-24 13:20:02 +0200 (Wed, 24 Sep 2014) | 7 lines
Updated the chi2 check in the
Frame_order.test_cam_qr_int_pseudo_ellipse_free_rotor_rdc system test.
This test is not normally run as it blacklisted and duplicates the coverage
of other tests. However
its chi-squared value check had not been updated for a while and hence the
test fails when
explicitly run.
........
r26003 | bugman | 2014-09-24 13:25:34 +0200 (Wed, 24 Sep 2014) | 5 lines
Updated all of the SciPy quadratic integration frame order target functions.
The pivot point is now handled quite different from back in May when these
functions were deleted.
........
r26004 | bugman | 2014-09-24 13:36:08 +0200 (Wed, 24 Sep 2014) | 3 lines
Missing imports for the SciPy quadratic integration function for the PCS in
lib.frame_order.rotor.
........
r26005 | bugman | 2014-09-24 13:51:26 +0200 (Wed, 24 Sep 2014) | 7 lines
The Sobol' point counting is now turned off for the frame order
optimisation functions if none exist.
If the cdp.quad_int flag is set, then there will be no Sobol' points to
count. This
count_sobol_point() user feedback function will therefore not be called by
the minimise.calculate,
minimise.grid_search and minimise.execute user functions.
........
r26006 | bugman | 2014-09-24 14:05:21 +0200 (Wed, 24 Sep 2014) | 6 lines
Turned off optimisation for all of the Frame_order.test_cam_quad_int_*
system tests.
The SciPy quadratic integration is far too slow to be used in the test
suite. The simple call to
the minimise.calculate user function is sufficient for checking these
target functions.
........
r26007 | bugman | 2014-09-24 14:07:09 +0200 (Wed, 24 Sep 2014) | 7 lines
Updated all of the Scipy quadratic integration frame order target functions.
A number of the data structures in the target function class have been
redesigned since these target
functions were deleted back in May. All of the func_*_quad_int*() target
functions have been
updated for these changes.
........
r26008 | bugman | 2014-09-24 14:09:46 +0200 (Wed, 24 Sep 2014) | 5 lines
Missing imports for the lib.frame_order.matrix_ops module.
These are for the recently restored SciPy quadratic integration functions.
........
r26009 | bugman | 2014-09-24 14:10:40 +0200 (Wed, 24 Sep 2014) | 3 lines
Removal of debugging code that was accidentally deleted.
........
r26010 | bugman | 2014-09-24 14:36:39 +0200 (Wed, 24 Sep 2014) | 8 lines
Updated all of the chi2 value checks for the
Frame_order.test_cam_quad_int_* system tests.
This is only for those tests which use PCS data - the RDC only test chi2
values are the same as in
the Frame_order.test_cam_qr_int_* system tests. In all cases, the chi2
value is lower for the more
accurate SciPy quadratic integration as compared to the quasi-random Sobol'
integration, as
expected.
........
Added:
trunk/lib/frame_order/variables.py
- copied unchanged from r25964,
branches/frame_order_cleanup/lib/frame_order/variables.py
Removed:
trunk/specific_analyses/frame_order/variables.py
Modified:
trunk/ (props changed)
trunk/auto_analyses/frame_order.py
trunk/lib/frame_order/__init__.py
trunk/lib/frame_order/double_rotor.py
trunk/lib/frame_order/iso_cone.py
trunk/lib/frame_order/iso_cone_torsionless.py
trunk/lib/frame_order/matrix_ops.py
trunk/lib/frame_order/pseudo_ellipse.py
trunk/lib/frame_order/pseudo_ellipse_torsionless.py
trunk/lib/frame_order/rotor.py
trunk/lib/frame_order/simulation.py
trunk/specific_analyses/frame_order/__init__.py
trunk/specific_analyses/frame_order/api.py
trunk/specific_analyses/frame_order/data.py
trunk/specific_analyses/frame_order/geometric.py
trunk/specific_analyses/frame_order/optimisation.py
trunk/specific_analyses/frame_order/parameters.py
trunk/specific_analyses/frame_order/uf.py
trunk/target_functions/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/iso_cone/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/multi_processor_test.py
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/rotor/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/rotor2/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/rotor2/pcs_only/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/rotor_2_state/frame_order.py
trunk/test_suite/system_tests/frame_order.py
trunk/test_suite/system_tests/scripts/frame_order/cam/base_script.py
trunk/test_suite/system_tests/scripts/frame_order/cam/double_rotor.py
trunk/test_suite/system_tests/scripts/frame_order/cam/double_rotor_large_angle.py
trunk/test_suite/system_tests/scripts/frame_order/cam/free_rotor.py
trunk/test_suite/system_tests/scripts/frame_order/cam/free_rotor2.py
trunk/test_suite/system_tests/scripts/frame_order/cam/free_rotor_missing_data.py
trunk/test_suite/system_tests/scripts/frame_order/cam/iso_cone.py
trunk/test_suite/system_tests/scripts/frame_order/cam/iso_cone_free_rotor.py
trunk/test_suite/system_tests/scripts/frame_order/cam/iso_cone_free_rotor2.py
trunk/test_suite/system_tests/scripts/frame_order/cam/iso_cone_torsionless.py
trunk/test_suite/system_tests/scripts/frame_order/cam/pseudo_ellipse.py
trunk/test_suite/system_tests/scripts/frame_order/cam/pseudo_ellipse2.py
trunk/test_suite/system_tests/scripts/frame_order/cam/pseudo_ellipse_free_rotor.py
trunk/test_suite/system_tests/scripts/frame_order/cam/pseudo_ellipse_torsionless.py
trunk/test_suite/system_tests/scripts/frame_order/cam/rigid.py
trunk/test_suite/system_tests/scripts/frame_order/cam/rotor.py
trunk/test_suite/system_tests/scripts/frame_order/cam/rotor2.py
trunk/test_suite/system_tests/scripts/frame_order/cam/rotor_2_state.py
trunk/user_functions/frame_order.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: trunk/auto_analyses/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/auto_analyses/frame_order.py?rev=27953&r1=27952&r2=27953&view=diff
Modified: trunk/lib/frame_order/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/__init__.py?rev=27953&r1=27952&r2=27953&view=diff
Modified: trunk/lib/frame_order/double_rotor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/double_rotor.py?rev=27953&r1=27952&r2=27953&view=diff
Modified: trunk/lib/frame_order/iso_cone.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/iso_cone.py?rev=27953&r1=27952&r2=27953&view=diff
Modified: trunk/lib/frame_order/iso_cone_torsionless.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/iso_cone_torsionless.py?rev=27953&r1=27952&r2=27953&view=diff
Modified: trunk/lib/frame_order/matrix_ops.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/matrix_ops.py?rev=27953&r1=27952&r2=27953&view=diff
Modified: trunk/lib/frame_order/pseudo_ellipse.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/pseudo_ellipse.py?rev=27953&r1=27952&r2=27953&view=diff
Modified: trunk/lib/frame_order/pseudo_ellipse_torsionless.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/pseudo_ellipse_torsionless.py?rev=27953&r1=27952&r2=27953&view=diff
Modified: trunk/lib/frame_order/rotor.py
[... 140 lines stripped ...]
r27953 - in /trunk: ./ auto_analyses/ lib/frame_order/ specific_analyses/frame_order/ target_functions/ test_suite/shared_da...