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://bug...@svn.gna.org/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 ...] _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits