relax SVN archive

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.

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.
.....

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.
.....

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.
.....

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.
.....

Merged revisions 25985 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r25985 | bugman | 2014-09-23 21:36:33 +0200 (Tue, 23 Sep 2014) | 9 lines

Massive speed up of the internal structural object add_model() method.

This speeds up the structure.add_model user function, as well as many internal relax operations on
the structural object. Instead of using the copy.deepcopy() function to duplicate an already
existing structural model, now new molecule container objects are created and then the individual
elements of the original molecule container data lists are copied one by one. This avoids copying a
lot of internal Python junk and hence the copying operation is now orders of magnitude faster.
........

Massive speed up of the internal structural object add_model() method.

This speeds up the structure.add_model user function, as well as many internal relax operations on
the structural object. Instead of using the copy.deepcopy() function to duplicate an already
existing structural model, now new molecule container objects are created and then the individual
elements of the original molecule container data lists are copied one by one. This avoids copying a
lot of internal Python junk and hence the copying operation is now orders of magnitude faster.

Merged revisions 25982 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r25982 | tlinnet | 2014-09-23 20:06:27 +0200 (Tue, 23 Sep 2014) | 3 lines

Implemented the sampling sparseness instead of NI on the graph axis.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
........

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.

Implemented the sampling sparseness instead of NI on the graph axis.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.