relax SVN archive

Merged revisions 25790-25792,25794-25799,25804-25809,25811-25845,25862-25896 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r25790 | bugman | 2014-09-12 15:05:07 +0200 (Fri, 12 Sep 2014) | 13 lines

Added support for the model argument for the frame_order.pdb_model user function.

This argument is used to specify which of the models in an ensemble will be used to represent the
average domain position Monte Carlo simulations, as each simulation is encoded as a model, as well
as for the distribution of structures simulating the motion of the system. The argument is
therefore passed into the create_ave_pos() and create_distribution() functions of the
specific_analyses.frame_order.geometric module.

To handle all models being used in the non Monte Carlo simulation PDB file and only one in this
file, the internal structural object is copied twice. The second copy for the MC sims has all but
the chosen model deleted out of it.
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r25791 | bugman | 2014-09-12 15:19:16 +0200 (Fri, 12 Sep 2014) | 6 lines

Fix for the Frame_order.test_frame_order_pdb_model_ensemble system test.

More needed to be done to set up the Monte Carlo simulations - the monte_carlo.initial_values user
function call was required.
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r25792 | bugman | 2014-09-12 15:20:32 +0200 (Fri, 12 Sep 2014) | 6 lines

Modified the frame order sim_init_values() API method to handle missing optimisation data.

The monte_carlo.initial_values user function was failing if optimisation had not been performed.
This is now caught and handled correctly.
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r25794 | bugman | 2014-09-12 15:30:26 +0200 (Fri, 12 Sep 2014) | 6 lines

Created the Frame_order.test_frame_order_pdb_model_failed_pivot system test.

This simply shows how the frame_order.pdb_model user function currently fails if the optimised pivot
point is outside of the PDB coordinate limits of "%8.3f".
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r25795 | bugman | 2014-09-12 15:45:45 +0200 (Fri, 12 Sep 2014) | 11 lines

The frame_order.pdb_model user function can now properly handle a failed pivot optimisation.

This is when the pivot point optimises to a coordinate outside of the PDB limits.

Now all calls to specific_analyses.frame_order.data.generate_pivot() from the module
specific_analyses.frame_order.geometric set the pdb_limit flag to True. This allows all
representation objects to be within the PDB limits. The algorithm in generate_pivot() has been
extended to allow higher positive values, as the real PDB limits are [-999.999, 9999.999]. And a
RelaxWarning is called when the pivot is outside to tell the user about it.
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r25796 | bugman | 2014-09-12 15:59:00 +0200 (Fri, 12 Sep 2014) | 17 lines

Reverted r25767 as this was rubbish, the frame_order.pivot user function updates the model itself.

The command used was:
svn merge -r25767:r25766 .

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r25767 | bugman | 2014-09-12 10:08:13 +0200 (Fri, 12 Sep 2014) | 6 lines
Changed paths:
M /branches/frame_order_cleanup/specific_analyses/frame_order/uf.py

Added a call to check_pivot() to the frame_order.select_model user function.

This is to prevent this user function from being called before the pivot has been set, as otherwise
the parameter vector will be incorrectly set up.
.....
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r25797 | bugman | 2014-09-12 16:06:38 +0200 (Fri, 12 Sep 2014) | 6 lines

Modified the frame order auto-analysis to be more fail-safe.

Almost all of the protocol is now within a try-finally block so that the execution lock will always
be released.
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r25798 | bugman | 2014-09-12 16:50:28 +0200 (Fri, 12 Sep 2014) | 7 lines

Fix for the specific_analyses.frame_order.data.pivot_fixed() function.

This was recently introduced (r25763) when the check for PCS data was removed from this function.
To fix the problem, instead of calling base_data_types() to see if PCS data is present, the
cdp.pcs_ids data structure is checked instead.
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r25799 | bugman | 2014-09-12 16:55:53 +0200 (Fri, 12 Sep 2014) | 6 lines

Fix for the model argument for the frame_order.pdb_model user function.

The deletion of structural models for the Monte Carlo simulations in the average domain position
representation now only happen if more than one model exists.
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r25804 | bugman | 2014-09-12 17:10:55 +0200 (Fri, 12 Sep 2014) | 6 lines

Modified the Frame_order.test_frame_order_pdb_model_failed_pivot system test.

This is to show that the frame_order.pdb_model user function fails if the pivot is close to but
still within the PDB coordinate limits.
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r25805 | bugman | 2014-09-12 17:13:19 +0200 (Fri, 12 Sep 2014) | 6 lines

Modified the pivot position checking in specific_analyses.frame_order.data.generate_pivot().

Now the pivot is shifted to be within the limits shrunk by 100 Angstrom. This allows any PDB
representation created by the frame_order.pdb_model user function to be within the PDB limits.
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r25806 | bugman | 2014-09-12 17:21:08 +0200 (Fri, 12 Sep 2014) | 6 lines

Fix for the axis permutation protocol in the frame order auto-analysis.

If a results file was found for one of the permutations, a return from the function would occur.
The result is that the other permutations would not be loaded or optimised.
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r25807 | bugman | 2014-09-12 17:31:20 +0200 (Fri, 12 Sep 2014) | 5 lines

Fix for the RelaxError raised by the frame_order.select_model user function.

This is the error if the model name is incorrect.
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r25808 | bugman | 2014-09-12 17:33:54 +0200 (Fri, 12 Sep 2014) | 6 lines

Created the Frame_order.test_pseudo_ellipse_zero_cone_angle system test.

This is to catch for a bug in optimisation when the cone_theta_x is set to zero in the
pseudo-ellipse models.
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r25809 | bugman | 2014-09-12 17:35:47 +0200 (Fri, 12 Sep 2014) | 7 lines

Bug fix for the lib.frame_order.pseudo_ellipse.tmax_pseudo_ellipse_array() function.

The problem was that when theta_x or theta_y were zero, the floating point value of 0.0 would be
returned. This is the incorrect behaviour as the returned value must be an array matching the
dimensions of the phi angle array argument.
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r25811 | bugman | 2014-09-12 18:07:20 +0200 (Fri, 12 Sep 2014) | 5 lines

Fix for the Pseudo_elliptic cone object for when the cone angles are zero.

The Pseudo_elliptic.phi_max() method now avoids a divide by zero error.
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r25812 | bugman | 2014-09-12 18:42:47 +0200 (Fri, 12 Sep 2014) | 6 lines

Updates for all of the Frame_order.test_axis_perm_* system tests.

The axis permutations and angle permutations are now performed correctly within the tests
themselves. This allows the tests to pass.
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r25813 | bugman | 2014-09-12 19:03:09 +0200 (Fri, 12 Sep 2014) | 6 lines

Modified the Frame_order.test_pseudo_ellipse_zero_cone_angle system test to be quick.

Now that the test passes, the optimisation needs to be short. So a maximum of two iterations are
now set. Otherwise the test would take hours to complete.
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r25814 | bugman | 2014-09-12 19:22:19 +0200 (Fri, 12 Sep 2014) | 3 lines

Small speed up of the Frame_order.test_auto_analysis system test.
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r25815 | bugman | 2014-09-14 11:33:37 +0200 (Sun, 14 Sep 2014) | 3 lines

Alphabetical ordering of most of the Frame_order system tests.
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r25816 | bugman | 2014-09-14 11:39:14 +0200 (Sun, 14 Sep 2014) | 6 lines

Created the very simple Frame_order.test_num_int_points system test.

This simply creates a data pipe and calls the frame_order.num_int_pts user function to test its
operation. This is to increase the test suite coverage of this user function.
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r25817 | bugman | 2014-09-14 11:54:58 +0200 (Sun, 14 Sep 2014) | 6 lines

Created the Frame_order.test_num_int_pts2 system test.

This checks the operation of the frame_order.num_int_pts user function when only the model has been
chosen.
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r25818 | bugman | 2014-09-14 12:01:49 +0200 (Sun, 14 Sep 2014) | 3 lines

Renamed the Frame_order.test_num_int_points system test to Frame_order.test_num_int_pts.
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r25819 | bugman | 2014-09-14 12:48:27 +0200 (Sun, 14 Sep 2014) | 6 lines

Created the check_domain() function for the frame order analysis.

This is in the specific_analyses.frame_order.checks module. The function checks that the reference
domain has been specified.
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r25820 | bugman | 2014-09-14 12:56:20 +0200 (Sun, 14 Sep 2014) | 6 lines

Created the check_model() function for the frame order analysis.

This is in the specific_analyses.frame_order.checks module. The function checks that the frame
order model has been selected via the frame_order.select_model user function.
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r25821 | bugman | 2014-09-14 12:58:39 +0200 (Sun, 14 Sep 2014) | 3 lines

Fixes for the new check_domain() and check_model() frame order functions.
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r25822 | bugman | 2014-09-14 13:01:01 +0200 (Sun, 14 Sep 2014) | 3 lines

The frame_order.ref_domain user function backend now uses the check_domain() function.
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r25823 | bugman | 2014-09-14 13:13:40 +0200 (Sun, 14 Sep 2014) | 6 lines

Created the check_parameters() function for the frame order analysis.

This is in the specific_analyses.frame_order.checks module. The function checks that the frame
order parameters have been set up and have values.
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r25824 | bugman | 2014-09-14 13:14:51 +0200 (Sun, 14 Sep 2014) | 6 lines

Created the Frame_order.test_num_int_pts3 system test.

This checks the operation of the frame_order.num_int_pts user function when the model has been and
the frame order parameters have been set up.
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r25825 | bugman | 2014-09-14 13:22:08 +0200 (Sun, 14 Sep 2014) | 7 lines

Created the Frame_order.test_count_sobol_points system test.

This will test that the frame_order.num_int_pts user function can correctly count the number of
Sobol' integration points used for the current set of parameter values. This
frame_order.num_int_pts functionality does not exist yet.
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r25826 | bugman | 2014-09-14 14:43:07 +0200 (Sun, 14 Sep 2014) | 7 lines

Implementation of the specific_analyses.frame_order.optimisation.count_sobol_points() function.

This is used by the frame_order.num_int_pts user function to provide a printout of the number of
Sobol' integration points used for the current parameter values. This is to provide user feedback
so that it is know if enough Sobol' points have been used.
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r25827 | bugman | 2014-09-14 14:44:49 +0200 (Sun, 14 Sep 2014) | 6 lines

Modified the Frame_order.test_count_sobol_points system test.

The number of points has been massively decreased as generating Sobol' points takes a long time, and
the check for the number of used Sobol' points has been set to the real value.
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r25828 | bugman | 2014-09-14 14:46:58 +0200 (Sun, 14 Sep 2014) | 6 lines

Created the Frame_order.test_count_sobol_points2 system test.

This checks the operation of the frame_order.count_sobol_points user function. As this user
function has not been implemented yet, the test currently fails.
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r25829 | bugman | 2014-09-14 14:56:40 +0200 (Sun, 14 Sep 2014) | 6 lines

Created the frame_order.count_sobol_points user function.

This is simply a frontend to the new specific_analyses.frame_order.optimisation.count_sobol_points()
function.
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r25830 | bugman | 2014-09-14 14:57:04 +0200 (Sun, 14 Sep 2014) | 3 lines

Updated the Frame_order.test_count_sobol_points2 system test for the correct number of Sobol' points.
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r25831 | bugman | 2014-09-14 15:01:35 +0200 (Sun, 14 Sep 2014) | 6 lines

Created the Frame_order.test_count_sobol_points_rigid system test.

This is to demonstrate a failure of the frame_order.test_count_sobol_points user function when
applied to the rigid frame order model.
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r25832 | bugman | 2014-09-14 15:07:22 +0200 (Sun, 14 Sep 2014) | 5 lines

Fix for the frame_order.count_sobol_points user function for the rigid model.

This model is now caught at the start, a message printed out, and the function exited.
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r25833 | bugman | 2014-09-14 15:08:46 +0200 (Sun, 14 Sep 2014) | 6 lines

Fix for the Frame_order.test_count_sobol_points_rigid system test.

This now checks that cdp.used_sobol_points does not exist for the rigid frame order model after a
call to the frame_order.count_sobol_points user function.
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r25834 | bugman | 2014-09-14 15:11:49 +0200 (Sun, 14 Sep 2014) | 5 lines

Created the Frame_order.test_count_sobol_points_rotor system test.

This is to test the frame_order.count_sobol_points user function for the rotor model.
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r25835 | bugman | 2014-09-14 15:13:46 +0200 (Sun, 14 Sep 2014) | 5 lines

Fix for the frame_order.count_sobol_points user function for the rotor model.

The sigma angles unpacking required a dimensionality collapse in the Sobol' angle data structure.
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r25836 | bugman | 2014-09-14 15:14:17 +0200 (Sun, 14 Sep 2014) | 3 lines

Updated the number of points to allow the Frame_order.test_count_sobol_points_rotor system test to pass.
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r25837 | bugman | 2014-09-14 15:38:39 +0200 (Sun, 14 Sep 2014) | 8 lines

The frame order count_sobol_points() function is now being called by all of minimise user functions.

This occurs at the end of the minimise.calculate, minimise.grid_search, and minimise.execute user
function backends to provide more feedback to the user as to the quality of the optimisation. To
avoid initialising the target function twice, the count_sobol_points() function now accepts the
initialised target function as an optional argument.
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r25838 | bugman | 2014-09-14 15:41:15 +0200 (Sun, 14 Sep 2014) | 6 lines

Created the Frame_order.test_count_sobol_points_free_rotor system test.

This is to demonstrate that the frame_order.count_sobol_points user function currently fails for the
free-rotor model.
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r25839 | bugman | 2014-09-14 15:44:09 +0200 (Sun, 14 Sep 2014) | 6 lines

Fix for the frame_order.count_sobol_points user function for the free-rotor models.

The torsion angle is now correctly handled as the 3 free-rotor models do not have cdp.cone_sigma_max
set.
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r25840 | bugman | 2014-09-14 15:44:45 +0200 (Sun, 14 Sep 2014) | 5 lines

Updated the number of points in the Frame_order.test_count_sobol_points_free_rotor system test.

This is to allow the test to pass.
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r25841 | bugman | 2014-09-14 15:51:45 +0200 (Sun, 14 Sep 2014) | 6 lines

Fix for the frame order count_sobol_points() function.

The checks for the model, parameter and domain set up must come first, before cdp.model is accessed.
Otherwise the frame_order.num_int_pts user function will often fail.
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r25842 | bugman | 2014-09-14 15:58:19 +0200 (Sun, 14 Sep 2014) | 7 lines

Fix for the frame order count_sobol_points() function.

The free-rotor isotropic cone model was incorrectly handled, as the cone parameter is 'cone_s1' and
not 'cone_theta'. The order parameter is now converted to angle before checking if the Sobol' point
is outside of the cone or not.
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r25843 | bugman | 2014-09-14 16:03:44 +0200 (Sun, 14 Sep 2014) | 6 lines

More fixed for the frame order count_sobol_points() function.

The torsion angle for the torsionless models is no longer accessed, and the cone_theta parameter is
only accessed for models with this parameter.
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r25844 | bugman | 2014-09-14 16:51:00 +0200 (Sun, 14 Sep 2014) | 6 lines

Created the Frame_order.test_count_sobol_points_iso_cone_free_rotor system test.

This is to test the frame_order.count_sobol_points user function for the free-rotor isotropic cone
model.
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r25845 | bugman | 2014-09-14 17:19:59 +0200 (Sun, 14 Sep 2014) | 6 lines

Fix for the frame order count_sobol_points() function.

The torsion angle ranges from -pi to pi, so the absolute value needs to be checked, just as in the
lib.frame_order modules.
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r25862 | bugman | 2014-09-17 11:05:28 +0200 (Wed, 17 Sep 2014) | 5 lines

Updates for the number of Sobol' points in the Frame_order.test_count_sobol_points_* system tests.

This is simply to allow all Frame_order system tests to pass.
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r25863 | bugman | 2014-09-17 17:11:12 +0200 (Wed, 17 Sep 2014) | 9 lines

Redesigned the frame_order.num_int_pts user function frontend for the oversampling idea.

The use of the quasi-random Sobol' sequence for numerical PCS integration will be modified to use
the concept of oversampling. Instead of specifying the exact number of points in the Sobol'
sequence and then removing points outside of the current parameter values, the algorithm will
oversample as N * Ov * 10**M, where N is the maximum number of Sobol' points to be used for the
integration, Ov is the oversampling factor, and M is the number of dimensions or torsion-tilt angles
used in the system. The aim is to try to use the maximum number of points N for all frame order
models and all ranges of dynamics.
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r25864 | bugman | 2014-09-17 17:11:14 +0200 (Wed, 17 Sep 2014) | 5 lines

Renamed the frame_order.num_int_pts user function to frame_order.sobol_setup.

The user function no longer specifies the number of integration points. Instead it now specifies
the maximum number of points N and oversampling factor Ov used to generate the oversampled Sobol'
sequence.
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r25865 | bugman | 2014-09-17 17:11:16 +0200 (Wed, 17 Sep 2014) | 1 line

Small fix for the frame_order.sobol_setup user function backend.
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r25866 | bugman | 2014-09-17 17:11:18 +0200 (Wed, 17 Sep 2014) | 1 line

Implemented the Sobol' sequence oversampling in the frame order target function class.
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r25867 | bugman | 2014-09-17 17:11:20 +0200 (Wed, 17 Sep 2014) | 7 lines

Converted all of the specific_analyses.frame_order package to the Sobol' point oversampling design.

The correct values are now sent into the target function and all references to cdp.num_int_pts has
been replaced with the cdp.sobol_max_points and cdp.sobol_oversample pair of variables.

The frame_order.count_sobol_points user function backend has also been updated to show the total
number of oversampling points and the number of points used.
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r25868 | bugman | 2014-09-17 17:11:21 +0200 (Wed, 17 Sep 2014) | 3 lines

The frame_order.count_sobol_points user function now shows more information.

The maximum number and oversampling factors are now also printed out for maximum user feedback.
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r25869 | bugman | 2014-09-17 17:11:23 +0200 (Wed, 17 Sep 2014) | 1 line

Improved the print out formatting for the count_sobol_points() frame order function.
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r25870 | bugman | 2014-09-17 17:11:25 +0200 (Wed, 17 Sep 2014) | 4 lines

The frame order target function now passes the maximum number of Sobol' points to the relax library.

The value is being passed into the lib.frame_order.*.pcs_numeric_int_*() functions, though it is not
used set.
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r25871 | bugman | 2014-09-17 17:11:26 +0200 (Wed, 17 Sep 2014) | 1 line

Fix for the percentage calculation for the frame order count_sobol_points() function.
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r25872 | bugman | 2014-09-17 17:11:28 +0200 (Wed, 17 Sep 2014) | 6 lines

Changed the creation of the Sobol' points in the frame order target function.

For increased accuracy of the numerical PCS integration, the first 1000 points of the Sobol'
sequence are now skipped to avoid any bias. For speed, the axis order of the Sobol' torsion-tilt
angles has been swapped so that the numpy.swapaxes() function call is no longer required in the
lib.frame_order.*.pcs_numeric_int_*() functions.
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r25873 | bugman | 2014-09-17 17:11:30 +0200 (Wed, 17 Sep 2014) | 1 line

Updated the frame order count_sobol_points() function to handle the swapped axis order.
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r25874 | bugman | 2014-09-17 17:11:32 +0200 (Wed, 17 Sep 2014) | 8 lines

Huge speed up for the generation of the Sobol' sequence data in the frame order target function.

The new Sobol_data class has been created and is instantiated in the module namespace as
target_function.frame_order.sobol_data. This is used to store all of the Sobol' sequence associated
data, including the torsion-tilt angles and all corresponding rotation matrices. When initialising
the target function, if the Sobol_data container holds the data for the same model and same total
number of Sobol' points, then the pre-existing data will be used rather than regenerating all the
data. This can save a huge amount of time.
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r25875 | bugman | 2014-09-17 17:11:33 +0200 (Wed, 17 Sep 2014) | 4 lines

Updated the frame order count_sobol_points() function to use the new Sobol_data container.

The Sobol' sequence data generated by the target function is now located at
target_functions.frame_order.sobol_data.
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r25876 | bugman | 2014-09-17 17:11:36 +0200 (Wed, 17 Sep 2014) | 5 lines

Updated all the lib.frame_order.*.pcs_numeric_int_*() functions for the new Sobol' point algorithm.

The functions now all accept the max_points argument and terminate the loop over the Sobol' points
once the maximum number of points has been reached. The calls to numpy.swapaxes() have also been
removed as this is now pre-performed by the target function initialisation.
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r25877 | bugman | 2014-09-17 17:11:37 +0200 (Wed, 17 Sep 2014) | 1 line

Changed the default oversampling factor from 100 to 1 in the frame_order.sobol_setup user function.
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r25878 | bugman | 2014-09-17 17:11:39 +0200 (Wed, 17 Sep 2014) | 5 lines

Converted the frame order auto-analysis to use the new frame_order.sobol_setup user function design.

The auto-analysis Optimisation_settings object has also been modified so that all num_int_pts
arguments and internal structures have been split into the two new sobol_max_points and
sobol_oversample names and objects.
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r25879 | bugman | 2014-09-17 17:11:41 +0200 (Wed, 17 Sep 2014) | 4 lines

Fix for the rigid frame order model for the recent frame_order.sobol_setup user function changes.

For this model, the number of Sobol' points normally is does not exist. This is now correctly
handled.
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r25880 | bugman | 2014-09-17 17:11:43 +0200 (Wed, 17 Sep 2014) | 4 lines

Created the sobol_setup() method for the frame order auto-analysis.

This is used to correctly handle the new design of the frame_order.sobol_setup user function
consistently throughout the protocol.
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r25881 | bugman | 2014-09-17 17:11:44 +0200 (Wed, 17 Sep 2014) | 3 lines

Updated the Frame_order.test_auto_analysis system test script.

This now uses the new auto-analysis Optimisation_settings object design.
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r25882 | bugman | 2014-09-17 17:11:46 +0200 (Wed, 17 Sep 2014) | 4 lines

Updated the Frame_order.test_count_sobol_points system test.

The call to the frame_order.num_int_pts user function was changed to
frame_order.sobol_setup.
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r25883 | bugman | 2014-09-17 17:11:49 +0200 (Wed, 17 Sep 2014) | 5 lines

Fixes for the Frame_order.test_count_sobol_points2 system test.

The test_suite/shared_data/frame_order/axis_permutations/cam_pseudo_ellipse.bz2 relax state file has
been manual edited to change the num_int_pts data pipe structure to sobol_max_points and to add the
new sobol_oversample variable.
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r25884 | bugman | 2014-09-17 17:11:51 +0200 (Wed, 17 Sep 2014) | 4 lines

Added a backwards compatibility hook for state and results files for the Sobol' sequence changes.

The data pipe num_int_pts variable is now renamed to sobol_max_points when present, and the
sobol_oversample variable is created and set to 1.
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r25885 | bugman | 2014-09-17 17:11:53 +0200 (Wed, 17 Sep 2014) | 4 lines

Updates to all of the Frame_order.test_count_sobol_points_* system tests.

The frame_order.sobol_setup user function is used to set a small maximum number of points (20) to
allow the tests to be fast. The value of 20 is also checked for to allow the tests to pass.
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r25886 | bugman | 2014-09-17 17:11:55 +0200 (Wed, 17 Sep 2014) | 4 lines

Renamed the cdp.used_sobol_points variable to sobol_points_used.

This is created by the count_sobol_points() frame order function. The name change is to match the
sobol_max_points and sobol_oversample variable names.
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r25887 | bugman | 2014-09-17 17:11:57 +0200 (Wed, 17 Sep 2014) | 4 lines

Renamed all the Frame_order.test_num_int_pts* system tests to Frame_order.test_sobol_setup*.

These system tests where for checking the operation of the old frame_order.num_int_pts user
function. But this is now the frame_order.sobol_setup user function.
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r25888 | bugman | 2014-09-17 17:11:59 +0200 (Wed, 17 Sep 2014) | 3 lines

Fix for all of the Frame_order.test_rigid_data_to_*_model system tests.

The frame_order.num_int_pts user function call was changed to frame_order.sobol_setup.
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r25889 | bugman | 2014-09-17 17:12:00 +0200 (Wed, 17 Sep 2014) | 3 lines

Updated the chi2 check in the Frame_order.test_rigid_data_to_free_rotor_model system test.

This value has changed due to the first 1000 points of the Sobol' sequence being skipped.
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r25890 | bugman | 2014-09-17 17:12:02 +0200 (Wed, 17 Sep 2014) | 4 lines

Fixes for all of the lib.frame_order.*.pcs_numeric_int_*_qrint() functions.

The loop over the Sobol' points was broken. As numpy.swapaxes() has been applied to the points
argument already, the loop needs to be over the second dimension of the points data structure.
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r25891 | bugman | 2014-09-17 17:12:05 +0200 (Wed, 17 Sep 2014) | 7 lines

Updates for all of the Frame_order.test_cam_* system tests.

The NUM_INT_PTS variable in the system tests scripts is now passed into the frame_order.sobol_setup
user function as the max_num argument. This number has also been changed so that the tests take a
reasonable amount of time. All chi2 value checks were updated. These were validated by increasing
the number of integration points and watching the chi2 value of the Frame_order.test_cam_*_pcs
version of the system tests head to zero.
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r25892 | bugman | 2014-09-17 17:12:06 +0200 (Wed, 17 Sep 2014) | 4 lines

Another update for the chi2 check in the Frame_order.test_rigid_data_to_free_rotor_model system test.

The previous commit used an incorrect value for the chi2. This new value is now much closer to the
original.
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r25893 | bugman | 2014-09-17 17:24:15 +0200 (Wed, 17 Sep 2014) | 7 lines

Turned down the verbosity of the update_model() frame order function.

The verbosity flag is now accepted and set to zero by the get_param_names() API method and
specific_analyses.frame_order.parameters.param_num() function. This removes a lot of useless
printouts from many different user functions.
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r25894 | bugman | 2014-09-17 17:31:01 +0200 (Wed, 17 Sep 2014) | 7 lines

Introduced the verbosity argument to the count_sobol_points() frame order function.

This is used to turn the printouts on or off. The optimisation code now calls this function with
the verbosity argument sent into the minimise.grid_search and minimise.execute user functions.
Hence the printouts are suppressed for Monte Carlo simulations.
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r25895 | bugman | 2014-09-17 17:35:58 +0200 (Wed, 17 Sep 2014) | 7 lines

Removed the axis system printout from the frame_order.pdb_model user function.

This is for the geometric representation of the frame order dynamics. The axis system is printed
out as the rotation matrix used for the lib.structure.geometric.generate_vector_residues() function
later on anyway. The change is to simplify the printouts.
........
r25896 | bugman | 2014-09-17 17:55:01 +0200 (Wed, 17 Sep 2014) | 3 lines

Editing of the docstring of the frame_order.sobol_setup user function.
........

Merged revisions 25713-25715,25720-25723,25725-25741,25744-25747,25749-25754,25760-25769 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

........
r25713 | bugman | 2014-09-09 14:24:13 +0200 (Tue, 09 Sep 2014) | 5 lines

Implemented the frame_order.permute_axes user function.

This is used to switch between local minima in the pseudo-elliptic frame order models.
........
r25714 | bugman | 2014-09-09 14:25:41 +0200 (Tue, 09 Sep 2014) | 7 lines

Fix for the Frame_order.test_axis_permutation system test.

The motional eigenframe in the old log file was not exactly correct and did not correspond exactly
to the Euler angles in the cam_pseudo_ellipse.bz2 results file in
test_suite/shared_data/frame_order/axis_permutations/.
........
r25715 | bugman | 2014-09-09 14:29:43 +0200 (Tue, 09 Sep 2014) | 6 lines

Extended the Frame_order.test_axis_permutation system test to check frame_order.permute_axes twice.

This will check that two calls to the frame_order.permute_axes user function will restore the
original parameter values.
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r25720 | bugman | 2014-09-09 19:13:17 +0200 (Tue, 09 Sep 2014) | 5 lines

The frame_order.permute_axes user function can now handle the torsionless pseudo-ellipse.

This model does not have the variable cdp.cone_sigma_max set.
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r25721 | bugman | 2014-09-09 19:18:46 +0200 (Tue, 09 Sep 2014) | 5 lines

Fix for the frame_order.permute_axes user function for the torsionless pseudo-ellipse.

This should have been part of the last commit.
........
r25722 | bugman | 2014-09-09 19:33:39 +0200 (Tue, 09 Sep 2014) | 8 lines

Added support for axis permutations in the frame order auto-analysis.

This is done by copying the data pipe of the already optimised pseudo-elliptic models, permuting the
axes, and performing another optimisation using all RDC and PCS data. This allows the second
solution for these pseudo-elliptic models to be found. The 2nd pipe is included in the model
selection step to allow the best solution for the model to be found.
........
r25723 | bugman | 2014-09-09 19:39:36 +0200 (Tue, 09 Sep 2014) | 7 lines

Fix for the reading of old results files in the frame order auto-analysis.

The directory name is now processed by the model_directory() method. This will convert the spaces
to '_' and remove commas. Without this the already created files could not be found, if the model
name contains a space or comma.
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r25725 | bugman | 2014-09-09 21:12:30 +0200 (Tue, 09 Sep 2014) | 6 lines

Made the pivot point in the frame order PDB representation fail-proof.

If the pivot position was outside of the bounds [-1000, 1000], the PDB file creation would fail as
the record would be too long. So now the pivot is shifted to be in these bounds.
........
r25726 | bugman | 2014-09-10 08:46:29 +0200 (Wed, 10 Sep 2014) | 5 lines

The axis permutation step in the frame order auto-analysis is now always performed.

If an old results file was found, this step was accidentally skipped.
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r25727 | bugman | 2014-09-10 09:22:20 +0200 (Wed, 10 Sep 2014) | 3 lines

Added extensive printouts to the frame_order.permute_axes user function.
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r25728 | bugman | 2014-09-10 11:43:11 +0200 (Wed, 10 Sep 2014) | 7 lines

Redesigned the frame_order.permute_axes user function frontend.

Previously only cyclic permutations were considered, however non-cyclic permutations are also
allowed when accompanied by an axis inversion. Therefore 3 combinations exist with cone_theta_x <=
cone_theta_y, or 2 when the current combination is excluded.
........
r25729 | bugman | 2014-09-10 13:21:28 +0200 (Wed, 10 Sep 2014) | 10 lines

Created 6 system tests for the frame_order.permute_axes user function.

This covers the 3 starting conditions (x<y<z, x<z<y, z<x<y) and the two permutations ('A' and 'B')
for each of these which do not include the starting permutation. They replace the original
Frame_order.test_axis_permutation system test with the tests
Frame_order.test_axis_perm_x_le_y_le_z_permA, Frame_order.test_axis_perm_x_le_y_le_z_permB,
Frame_order.test_axis_perm_x_le_z_le_y_permA, Frame_order.test_axis_perm_x_le_z_le_y_permB,
Frame_order.test_axis_perm_z_le_x_le_y_permA, and Frame_order.test_axis_perm_z_le_x_le_y_permB.
........
r25730 | bugman | 2014-09-10 13:41:33 +0200 (Wed, 10 Sep 2014) | 8 lines

Implemented the new frame_order.permute_axes backend.

The 3 starting conditions x<y<z, x<z<y, and z<x<y and the two permutations 'A' and 'B' (for each of
these which do not include the starting permutation) are now supported. For these 6 combinations,
the axis and order parameter permutation and the z-axis inversion are selected and applied to the
current system.
........
r25731 | bugman | 2014-09-10 13:43:41 +0200 (Wed, 10 Sep 2014) | 5 lines

Removed the second permutation from the 6 Frame_order.test_axis_perm_* system tests.

A second identical permutation does not necessarily restore the original state.
........
r25732 | bugman | 2014-09-10 13:49:20 +0200 (Wed, 10 Sep 2014) | 5 lines

Fix for the frame_order.permute_axes for the torsionless pseudo-ellipse model.

The data structure cdp.cone_sigma_max does not exist in this model as cone_sigma_max == 0.0.
........
r25733 | bugman | 2014-09-10 13:57:03 +0200 (Wed, 10 Sep 2014) | 7 lines

Modified the frame order auto-analysis axis permutation algorithm to handle both permutations.

Instead of creating one additional data pipe for the permutations, two are now created for the
permutations 'A' and 'B'. This allows all 3 solutions for the pseudo-elliptic models to be
explored and included in the final model selection process.
........
r25734 | bugman | 2014-09-10 14:20:43 +0200 (Wed, 10 Sep 2014) | 5 lines

Fix for the Frame_order.test_axis_perm_x_le_z_le_y_permB system test.

The permuted z-axis needs to be inverted in the test.
........
r25735 | bugman | 2014-09-10 14:24:58 +0200 (Wed, 10 Sep 2014) | 8 lines

Many fixes for the frame_order.permute_axes user function.

The z-axis inversion is now encoded into a 3D numpy array as the index of the new z-axis position
needs to be stored. The cone_theta_x, cone_theta_y and cone_sigma_max parameters are now permuted
in reverse 'perm' data structure by calling its index() method. And the cone_theta_x - cone_theta_y
to y-axis - x-axis switch has been removed (this may need to be reintroduced later).
........
r25736 | bugman | 2014-09-10 14:41:23 +0200 (Wed, 10 Sep 2014) | 6 lines

Fix for the axis permutation protocol in the frame order auto-analysis.

The pipe.copy user function does not switch pipes, therefore the pipe.switch user function is now
being called so that the correct pipe is being permuted and optimised.
........
r25737 | bugman | 2014-09-10 18:46:29 +0200 (Wed, 10 Sep 2014) | 9 lines

Created some test data files for visualising the frame order axis permutation.

This uses the CaM frame order synthetic data for the rotor model to visualise the pseudo-ellipse
frame order model axis permutations. The initial conversion sets the pseudo-ellipse torsion angle
cone_sigma_max to the rotor opening half-angle, and the pseudo-elliptic cone opening to close to
zero. Then the axis permutations are performed. All three solutions are optimised. PDB
representations before and after optimisation are included to illustrate any problems.
........
r25738 | bugman | 2014-09-10 21:33:37 +0200 (Wed, 10 Sep 2014) | 7 lines

Bug fix for the new frame_order.permute_axes user function.

The cone and torsion angles were not being correctly permuted. Now the direct permutation array is
being used. And the fact that cone_theta_x is a rotation along the y-axis and cone_theta_y along
the x-axis is taken into account.
........
r25739 | bugman | 2014-09-11 13:43:37 +0200 (Thu, 11 Sep 2014) | 8 lines

Redesign of the axis permutation algorithm of the frame_order.permute_axes user function.

Instead of tracking the fact that cone_theta_x is a rotation around the y-axis and cone_theta_y is
about the x-axis, now two permutation arrays are created - one for the three angles and one for the
axes. The permutation array values have also been completely changed as previously the incorrect
inverse permutation was coded into the algorithm.
........
r25740 | bugman | 2014-09-11 14:58:38 +0200 (Thu, 11 Sep 2014) | 6 lines

Updated the frame order pseudo-ellipse motion permutation test data.

This is for the CaM frame order rotor model synthetic data. The correct axis and cone angle
permutations of the frame_order.permute_axes user function are now being used and optimised.
........
r25741 | bugman | 2014-09-11 14:59:42 +0200 (Thu, 11 Sep 2014) | 5 lines

Renamed the pseudo-ellipse permutation directory to perm_pseudo_ellipse_x_le_y_le_z.

This is for the CaM frame order rotor model synthetic data.
........
r25744 | bugman | 2014-09-11 15:42:19 +0200 (Thu, 11 Sep 2014) | 5 lines

Fix for the frame_order.permute_axes user function.

One of the 6 permutations had the x and y axes switched (the x <= z <= y condition, permutation A).
........
r25745 | bugman | 2014-09-11 17:17:05 +0200 (Thu, 11 Sep 2014) | 8 lines

Visualisation files for all of the pseudo-ellipse permutations by frame_order.permute_axes.

This includes the x <= z <= y and z <= x <= y conditions (the previous files were for x <= y <= z).
In all permutation combinations, optimisation has been performed to demonstrate that these are all
local minima. These all approximate the rotor when using the CaM frame order rotor model synthetic
data.
........
r25746 | bugman | 2014-09-11 19:16:52 +0200 (Thu, 11 Sep 2014) | 8 lines

Added support for the isotopic cone models to the frame_order.permute_axes user function.

This is a simpler setup, but it uses the same permutation algorithm as derived for the
pseudo-ellipse models. Instead of setting the x and y cone angles separately, they are instead
averaged. And as the cone axis is undefined in the xy plane, the axis has been randomly selected as
being the axis perpendicular to both the z-axis and the reference frame x-axis.
........
r25747 | bugman | 2014-09-11 19:19:18 +0200 (Thu, 11 Sep 2014) | 7 lines

Created set of files showing the axis permutation problem for the isotopic cone frame order model.

This shows that there are two minima. However one has a chi-squared value of ~1, and the other a
value of ~150. Nevertheless, the optimisation could be trapped in the non-global minimum so the
frame_order.permute_axes user function should be used for the isotopic cones as well, just in case.
........
r25749 | bugman | 2014-09-11 19:37:44 +0200 (Thu, 11 Sep 2014) | 7 lines

Created the other isotropic cone condition z <= x = y.

As there are no constraints in this model, this condition should not result in any major
differences, just the size of the cone being different and the optimisation having to decrease the
cone angle significantly to mimic the rotor.
........
r25750 | bugman | 2014-09-11 19:43:45 +0200 (Thu, 11 Sep 2014) | 5 lines

Added the missing PDB files which should have been committed previously.

This are in test_suite/shared_data/frame_order/cam/rotor/perm_iso_cone_z_le_xy.
........
r25751 | bugman | 2014-09-11 19:44:22 +0200 (Thu, 11 Sep 2014) | 5 lines

Added the missing PDB files which should have been committed previously.

This are in test_suite/shared_data/frame_order/cam/rotor/perm_iso_cone_xy_le_z/.
........
r25752 | bugman | 2014-09-11 19:52:47 +0200 (Thu, 11 Sep 2014) | 7 lines

Modified the frame order auto-analysis.

The axis permutation algorithm is now performed on all isotopic cone and pseudo-ellipse models.
This is just in case the non-global minima was found in the original optimisation. The isotropic
cone models possess two local minima whereas the pseudo-ellipse models possess three local minima.
........
r25753 | bugman | 2014-09-11 19:57:46 +0200 (Thu, 11 Sep 2014) | 5 lines

Simplified the optimisation in the axis permutation part of the frame order auto-analysis.

Only the last, highest quality setting is used for optimisation.
........
r25754 | bugman | 2014-09-11 20:30:12 +0200 (Thu, 11 Sep 2014) | 6 lines

Fix for the axis permutation protocol in the frame order auto-analysis.

This would fail if a results file for the permuted model already exists as the pipe.copy user
function call was being performed too early.
........
r25760 | bugman | 2014-09-11 21:56:47 +0200 (Thu, 11 Sep 2014) | 3 lines

Created set of files for the axis permutation of the torsionless isotopic cone frame order model.
........
r25761 | bugman | 2014-09-12 09:35:32 +0200 (Fri, 12 Sep 2014) | 7 lines

Created an initial Frame_order.test_frame_order_pdb_model_ensemble system test.

This is to check the operation of the frame_order.pdb_model user function when an ensemble of
structures is encountered. However as this uses a very minimal number of user functions to set up
the system, a number of other minor bugs will probably be uncovered.
........
r25762 | bugman | 2014-09-12 09:45:00 +0200 (Fri, 12 Sep 2014) | 6 lines

Added printouts to the specific_analyses.frame_order.parameters.update_model() function.

This is to make it easier to understand why certain things fail due to the system not being fully
set up.
........
r25763 | bugman | 2014-09-12 09:49:37 +0200 (Fri, 12 Sep 2014) | 6 lines

Simplified the operation of the frame_order.select_model user function.

This is by removing the check of PCS data from the specific_analyses.frame_order.data.pivot_fixed()
function using the base_data_types() function call. This allows the model to be set up more easily.
........
r25764 | bugman | 2014-09-12 09:54:31 +0200 (Fri, 12 Sep 2014) | 5 lines

Modified the frame order check_pivot() function to operate on any data pipe.

The function now accepts the pipe_name argument so that checks can happen on any data pipe.
........
r25765 | bugman | 2014-09-12 09:57:12 +0200 (Fri, 12 Sep 2014) | 5 lines

Missing imports in the specific_analyses.frame_order.checks module.

This is from the recent pipe_name argument addition in the check_pivot() function.
........
r25766 | bugman | 2014-09-12 09:58:37 +0200 (Fri, 12 Sep 2014) | 6 lines

The frame order generate_pivot() function can now handle no pivot being present.

At the start of this specific_analyses.frame_order.data module function, the check_pivot() function
is being called to make sure that a pivot is present.
........
r25767 | bugman | 2014-09-12 10:08:13 +0200 (Fri, 12 Sep 2014) | 6 lines

Added a call to check_pivot() to the frame_order.select_model user function.

This is to prevent this user function from being called before the pivot has been set, as otherwise
the parameter vector will be incorrectly set up.
........
r25768 | bugman | 2014-09-12 10:12:00 +0200 (Fri, 12 Sep 2014) | 5 lines

Modified the Frame_order.test_frame_order_pdb_model_ensemble system test so it is set up correctly.

The pivot point and moving domain are now specified.
........
r25769 | bugman | 2014-09-12 10:14:16 +0200 (Fri, 12 Sep 2014) | 7 lines

Added Monte Carlo simulations to the Frame_order.test_frame_order_pdb_model_ensemble system test.

This is only setting up Monte Carlo simulation data structures via the monte_carlo.setup user
function. This demonstrates a failure of the frame_order.pdb_model user function when an ensemble
of structures is present with Monte Carlo simulations.
........

Merged revisions 24839-24840,25299-25301,25402,25416,25536-25537,25710-25711 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

........
r24839 | bugman | 2014-07-30 17:27:07 +0200 (Wed, 30 Jul 2014) | 8 lines

Fixes for the removal of the RDC data checks from the frame order optimisation functions.

The specific analysis API method overfit_deselect() has now been created to deselect spins which do
not have PCS data or interatomic data containers missing RDC data. The handling of deselected spins
and interatomic data containers is now also correctly handled throughout the frame order specific
code.
........
r24840 | bugman | 2014-07-30 17:27:48 +0200 (Wed, 30 Jul 2014) | 3 lines

Enabled pivot optimisation in the full_analysis.py script for the CaM frame order test data.
........
r25299 | bugman | 2014-08-26 17:31:19 +0200 (Tue, 26 Aug 2014) | 6 lines

The frame order auto-analysis now calls the time() user function.

This is used at the start of each model section, as well as at the very start and very end of the
analysis. This feedback is needed for the user to be able to optimise the optimisation settings.
........
r25300 | bugman | 2014-08-26 17:49:16 +0200 (Tue, 26 Aug 2014) | 8 lines

Major bugfix for the frame order auto-analysis.

The algorithm of using a PCS data subset of a few selected residues to find an initial parameter
estimate followed by using all PCS data was badly implemented. The use of the PCS subset caused
most spin systems to be deselected, however they remained deselected once all data was being used.
So the result was that only the spin subset was ever being used in the analysis.
........
r25301 | bugman | 2014-08-26 17:52:19 +0200 (Tue, 26 Aug 2014) | 3 lines

Removed some printouts accidentally committed in the previous revision.
........
r25402 | bugman | 2014-08-28 18:45:24 +0200 (Thu, 28 Aug 2014) | 3 lines

Fix for the recent lib.period_table and lib.physical_constant module changes.
........
r25416 | bugman | 2014-08-29 10:11:58 +0200 (Fri, 29 Aug 2014) | 7 lines

Created the model_directory() method for the frame order auto-analysis.

This is used to create the full path for saving model specific files. It replaces spaces with
underscores in the path and removes all commas. The commas in the path appear to be fatal for
certain PyMOL versions when viewing the frame order representation.
........
r25536 | bugman | 2014-09-02 11:35:22 +0200 (Tue, 02 Sep 2014) | 3 lines

The frame order auto-analysis results printout has been extended to include the pivot point.
........
r25537 | bugman | 2014-09-02 11:39:40 +0200 (Tue, 02 Sep 2014) | 7 lines

Change to the parameter nesting in the frame order auto-analysis.

The pivot is now taken from the rotor model for all other models. Taking the pivot point from the
isotropic cone model is not a good idea as there are situations where the pivot point optimisation
catastrophically fails, sending the point many tens or hundreds of Angstrom away from the molecule.
........
r25710 | bugman | 2014-09-09 09:18:49 +0200 (Tue, 09 Sep 2014) | 10 lines

Copied a frame order results file for testing axis permutations.

The command used was:
svn cp test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order.bz2@r23644 test_suite/shared_data/frame_order/axis_permutations/cam_pseudo_ellipse.bz2

This is from the test_suite/shared_data/frame_order/cam/pseudo_ellipse/ directory. The optimisation
results back at r23644 were identified to have failed, in that it found the alternative minimum.
The pseudo-ellipse model as two minima in the space, and in this case the global minimum was missed.
........
r25711 | bugman | 2014-09-09 10:55:41 +0200 (Tue, 09 Sep 2014) | 5 lines

Created the Frame_order.test_axis_permutation system test.

This is to test the operation of the yet-to-be implemented frame_order.permute_axes user function.
........

Merged revisions 24819-24823,24832-24836 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

........
r24819 | bugman | 2014-07-29 18:43:34 +0200 (Tue, 29 Jul 2014) | 5 lines

Missing import in the lib.frame_order.double_rotor module.

This was identified by the new Frame_order.test_auto_analysis system test.
........
r24820 | bugman | 2014-07-30 08:46:03 +0200 (Wed, 30 Jul 2014) | 7 lines

Updates and fixes for the frame order auto-analysis.

The custom grid setup now works for the new reduced parameter set models and the double rotor model
is now also included. The cone axis alpha angle to spherical angle conversion has had a bug
removed. And some of the printouts are now more detailed.
........
r24821 | bugman | 2014-07-30 09:34:22 +0200 (Wed, 30 Jul 2014) | 8 lines

Redesigned the Frame_order.test_auto_analysis system test.

This now uses a hypothetical new Optimisation_settings object from the frame order auto-analysis
module for holding all of the grid search, zooming grid search and minimisation settings. This will
allow for far greater user control of the settings and hugely simplify the auto-analysis interface
by decreasing the number of input arguments. It should also be less confusing.
........
r24822 | bugman | 2014-07-30 11:07:47 +0200 (Wed, 30 Jul 2014) | 16 lines

Implementation of the Optimisation_settings object in the frame order auto-analysis.

This object holds all of the grid search, zooming grid search, and minimisation settings. It
provides the add_grid() and add_min() methods to allow the user to add successive iterations of
optimisation and settings to the object. The loop_grid() and loop_min() methods are used to loop
over each iteration of each method. And the get_grid_inc(), get_grid_num_int_pts(),
get_grid_zoom_level(), get_min_algor(), get_min_func_tol() and get_min_num_int_pts() methods are
used to access the user defined settings.

The auto-analysis has been redesigned around this new concept. All of the optimisation arguments
have been replaced. Instead there are the opt_rigid, opt_subset, opt_full, and opt_mc arguments
which are expected to be instances of the Optimisation_settings object. The optimisation in the
auto-analysis is now more advanced in that more user optimisation settings are now available and
active.
........
r24823 | bugman | 2014-07-30 12:22:43 +0200 (Wed, 30 Jul 2014) | 9 lines

Added linear constraints for the pivot and average domain translation frame order parameters.

The pivot coordinates are constrained between -999 and 999 Angstrom and the translation between -500
and 500 Angstrom. This allows the frame_order.pdb_model user function to operate in the case of
failed models - often the free rotors fitting to torsionally restricted data - by preventing the PDB
coordinates from being out of the PDB format range. It should also speed up optimisation by
stopping the optimisation of failed models earlier.
........
r24832 | bugman | 2014-07-30 14:26:15 +0200 (Wed, 30 Jul 2014) | 8 lines

The frame order auto-analysis Optimisation_settings object now handles the maximum iterations.

The new max_iter argument has been added to the add_min() method, and the new get_min_max_iter()
method added to fetch the value. This is used in the auto-analysis to set the maximum number of
optimisation iterations in the minimise.execute user function calls. Limiting this will be of
greatest benefit for the test suite.
........
r24833 | bugman | 2014-07-30 14:27:47 +0200 (Wed, 30 Jul 2014) | 7 lines

Speed up of the Frame_order.test_auto_analysis system test.

This involves limiting the maximum number of optimisation steps to 20 for most parts (the rigid
model excluded so the average domain position is correctly found), and using the PCS subset data for
the full data set.
........
r24834 | bugman | 2014-07-30 14:36:03 +0200 (Wed, 30 Jul 2014) | 6 lines

Updated the full_analysis.py script for the CaM frame order test data.

This is for the recent changes to the auto-analysis with the Optimisation_settings object and for
the changes of this branch.
........
r24835 | bugman | 2014-07-30 14:38:21 +0200 (Wed, 30 Jul 2014) | 5 lines

Fix for the previous commit (r24834).

The results directory was incorrectly set.
........
r24836 | bugman | 2014-07-30 15:31:09 +0200 (Wed, 30 Jul 2014) | 10 lines

Removed the RDC data checks from the frame order optimisation.

This is in the minimise_setup_rdcs() and store_bc_data() functions of the
specific_analyses.frame_order.optimisation module, called before and after all optimisation. The
reason was identified by profiling - this check was adding significant amounts of time to the setup
and results unpacking parts of the optimisation. Specifically the interatomic_loop() function was
identified via profiling as the function requiring the most amount of cumulative time in the
Frame_order.test_auto_analysis system test (17 seconds out of a total of ~60 seconds).
........

Merged revisions 24778,24783-24784,24787,24798-24810,24814-24817 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

........
r24778 | bugman | 2014-07-27 10:40:21 +0200 (Sun, 27 Jul 2014) | 7 lines

Fixes for the CaM free-rotor pseudo-ellipse frame order model test data set.

This is for the constraint 0 <= theta_x <= theta_y <= pi, as the old data was created with theta_x
> theta_y. The new data is also of high quality using 20 million structures and numpy.float128 data
averaging.
........
r24783 | bugman | 2014-07-28 14:21:04 +0200 (Mon, 28 Jul 2014) | 5 lines

Created the lib.frame_order.rotor_axis.convert_axis_alpha_to_spherical() function.

This will convert the axis alpha angle to the equivalent spherical angles theta and phi.
........
r24784 | bugman | 2014-07-28 15:48:50 +0200 (Mon, 28 Jul 2014) | 5 lines

Renamed the lib.frame_order.rotor_axis module to lib.frame_order.conversions.

This module will be used for all sorts of frame order parameter conversions.
........
r24787 | bugman | 2014-07-28 16:29:59 +0200 (Mon, 28 Jul 2014) | 5 lines

Added the pipe_name argument to the specific_analyses.frame_order.data.generate_pivot() function.

This allows the pivot from data pipes other than the current one to be assembled and returned.
........
r24798 | bugman | 2014-07-29 11:39:10 +0200 (Tue, 29 Jul 2014) | 8 lines

Updated the frame order optimisation results for the CaM free rotor, pseudo-ellipse test data.

The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo simulations. The new
frame order representation files have been added to the repository, as well as the intermediate
state files.
........
r24799 | bugman | 2014-07-29 11:40:25 +0200 (Tue, 29 Jul 2014) | 8 lines

Updated the frame order optimisation results for the CaM torsionless, pseudo-ellipse test data.

The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo simulations. The new
frame order representation files have been added to the repository, as well as the intermediate
state files.
........
r24800 | bugman | 2014-07-29 11:58:19 +0200 (Tue, 29 Jul 2014) | 5 lines

Fix for the Frame_order.test_cam_pseudo_ellipse_free_rotor system test.

This is for the change of the X and Y cone opening angles.
........
r24801 | bugman | 2014-07-29 13:11:20 +0200 (Tue, 29 Jul 2014) | 14 lines

Redesign and expansion of the nested model parameter copying in the frame order auto-analysis.

The nested parameter protocol used to allow the analysis to complete in under 1,000,000 years was no
longer functional due to the switching to the axis alpha parameter to decrease parameter number and
redundancy. The copying of the average domain position for the free rotor models was also incorrect
as the dropping of the alpha Euler angle cause the translation parameters and beta and gamma angles
to change drastically.

The new protocol has been split into four methods for the average domain position, the pivot point,
the motional eigenframe and the parameters of ordering. These use the fact that the free rotor and
torsionless models are the two extrema of the models where the torsion angle is restricted. The
pivot copying is a new addition.
........
r24802 | bugman | 2014-07-29 13:58:14 +0200 (Tue, 29 Jul 2014) | 7 lines

Created the Frame_order.test_auto_analysis system test.

This will be an extremely quick run through of the frame order auto-analysis as this is not
currently tested. 1 Sobol' quasi-random integration point will be used for all models for speed.
The system test uses the rigid CaM test data to perform a full analysis.
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r24803 | bugman | 2014-07-29 13:59:39 +0200 (Tue, 29 Jul 2014) | 3 lines

Import fix for the frame order auto-analysis.
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r24804 | bugman | 2014-07-29 14:01:04 +0200 (Tue, 29 Jul 2014) | 3 lines

Alphabetical ordering of the imports in the frame order auto-analysis module.
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r24805 | bugman | 2014-07-29 14:06:14 +0200 (Tue, 29 Jul 2014) | 5 lines

Fixes for the backend script of the Frame_order.test_auto_analysis system test.

This includes a missing import and the removal of a long ago deleted user function.
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r24806 | bugman | 2014-07-29 14:08:11 +0200 (Tue, 29 Jul 2014) | 6 lines

Fix for the frame order auto-analysis for the call to the grid search user function.

This user function has been renamed to minimise.grid_search, however not all parts of the analysis
had been converted to the new name.
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r24807 | bugman | 2014-07-29 15:13:46 +0200 (Tue, 29 Jul 2014) | 6 lines

Created a method in the frame order auto-analysis to reorder the models.

This is needed as the nested model parameter copying protocol requires the simpler models to be
optimised first.
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r24808 | bugman | 2014-07-29 15:17:02 +0200 (Tue, 29 Jul 2014) | 5 lines

The Frame_order.test_auto_analysis system test now writes all files to the directory of ds.tmpdir.

This is to prevent the system test from dumping files in the current directory.
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r24809 | bugman | 2014-07-29 15:38:41 +0200 (Tue, 29 Jul 2014) | 5 lines

Modified the specific_analyses.frame_order.parameters.update_model() function.

This will no longer set all parameters to 0.0, excluding the pivot point.
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r24810 | bugman | 2014-07-29 16:07:28 +0200 (Tue, 29 Jul 2014) | 6 lines

Modified the specific_analyses.frame_order.parameters.assemble_param_vector() function.

This can now handle the case of no parameters being present. The corresponding elements of the
numpy array will consist of NaN values.
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r24814 | bugman | 2014-07-29 16:41:17 +0200 (Tue, 29 Jul 2014) | 10 lines

Better handling of unset parameters in the frame order optimisation functions.

The specific_analyses.frame_order.optimisation.target_fn_data_setup() and
specific_analyses.frame_order.parameters.assemble_param_vector() function both now accept the
unset_fail argument. This is set in both the calculate() and minimise() API methods. When set, a
RelaxError will be raised in the assemble_param_vector() function when a parameter has not been set
yet. This together with previous changes will prevent the frame order analysis from using 0.0 as a
starting value for unset parameters.
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r24815 | bugman | 2014-07-29 17:01:55 +0200 (Tue, 29 Jul 2014) | 7 lines

Fixes for all of the Frame_order.test_rigid_data_to_*_model system tests.

The base script now sets all parameter values so that the minimise.calculate user function can
operate. The two free rotor model chi-squared values have been updated as these are sensitive to
the motional eigenframe parameter values - these models can never approximate a rigid state.
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r24816 | bugman | 2014-07-29 17:38:31 +0200 (Tue, 29 Jul 2014) | 5 lines

Modified the optimisation of the rigid model in the frame order auto-analysis.

The grid search is now implemented as a zooming grid search.
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r24817 | bugman | 2014-07-29 18:03:37 +0200 (Tue, 29 Jul 2014) | 5 lines

Missing import in the lib.frame_order.rotor module.

This was identified by the new Frame_order.test_auto_analysis system test.
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Merged revisions 24731-24735,24754 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r24731 | bugman | 2014-07-24 18:53:53 +0200 (Thu, 24 Jul 2014) | 3 lines

Converted the frame_order_free_start.py script to use the zooming grid search.
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r24732 | bugman | 2014-07-24 19:01:00 +0200 (Thu, 24 Jul 2014) | 5 lines

Added lots of calls to the time user function to the frame_order_free_start.py.

This will be used to fine tune the frame order analysis on a cluster.
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r24733 | bugman | 2014-07-25 09:03:18 +0200 (Fri, 25 Jul 2014) | 7 lines

Increased the default grid bounds for the pivot parameters of the frame order models.

The pivot point is now searched for in a 50 Angstrom box and the pivot displacement for the double
motion models from 10 to 60 Angstroms. These were originally a 20 Angstrom box and 10 to 50
Angstroms. The larger grid is possible when combined with the new zooming grid search.
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r24734 | bugman | 2014-07-25 09:32:15 +0200 (Fri, 25 Jul 2014) | 8 lines

Updated the frame order optimisation results for the 2-site CaM test data fitting to the rotor model.

The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo simulations. The new
frame order representation files have been added to the repository, as well as the intermediate
state files.
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r24735 | bugman | 2014-07-25 09:36:43 +0200 (Fri, 25 Jul 2014) | 8 lines

Updated the frame order optimisation results for the CaM rotor test data.

The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo simulations. The new
frame order representation files have been added to the repository, as well as the intermediate
state files.
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r24754 | bugman | 2014-07-25 15:57:19 +0200 (Fri, 25 Jul 2014) | 8 lines

Updated the frame order optimisation results for the 2nd CaM rotor test data.

The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo simulations. The new
frame order representation files have been added to the repository, as well as the intermediate
state files.
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Merged revisions 24715-24717 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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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.
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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.
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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).
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Merged revisions 24709-24713 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r24709 | bugman | 2014-07-24 15:11:29 +0200 (Thu, 24 Jul 2014) | 3 lines

Some more fixes for the optimisation user function changes.
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r24710 | bugman | 2014-07-24 16:02:59 +0200 (Thu, 24 Jul 2014) | 7 lines

Removed the parameter scaling for the pivot point frame order parameters.

These were already removed from the frame_order_cleanup branch in the assemble_scaling_matrix()
function, however they were reintroduced accidentally via the parameter object where this
information is now defined. So this removes the scaling a second time.
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r24711 | bugman | 2014-07-24 16:04:13 +0200 (Thu, 24 Jul 2014) | 6 lines

Fixes for the parameter scaling changes in the trunk.

The scaling flag is no longer part of the specific analysis API optimisation methods. Instead the
pre-assembled scaling matrices are passed into all three API optimisation methods.
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r24712 | bugman | 2014-07-24 16:21:47 +0200 (Thu, 24 Jul 2014) | 5 lines

Implemented the frame order specific analysis API method print_model_title().

This is simply aliased from the API common method _print_model_title_global().
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r24713 | bugman | 2014-07-24 16:24:53 +0200 (Thu, 24 Jul 2014) | 5 lines

Fix for the grid search in the frame order analysis.

This is a recently introduced problem due to the changes of the zooming_grid_search branch.
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Merged revisions 24560-24561,24585-24586,24666-24667 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r24560 | bugman | 2014-07-18 10:26:01 +0200 (Fri, 18 Jul 2014) | 8 lines

Updated the frame order optimisation results for the CaM free rotor isotropic cone test data.

The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo simulations. The new
frame order representation files have been added to the repository, as well as the intermediate
state files.
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r24561 | bugman | 2014-07-18 10:30:09 +0200 (Fri, 18 Jul 2014) | 8 lines

Updated the frame order optimisation results for the CaM small angle rotor test data.

The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo simulations. The new
frame order representation files have been added to the repository, as well as the intermediate
state files.
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r24585 | bugman | 2014-07-21 16:07:58 +0200 (Mon, 21 Jul 2014) | 8 lines

Updated the frame order optimisation results for the 2nd CaM free rotor isotropic cone test data.

The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo simulations. The new
frame order representation files have been added to the repository, as well as the intermediate
state files.
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r24586 | bugman | 2014-07-21 16:10:51 +0200 (Mon, 21 Jul 2014) | 8 lines

Updated the frame order optimisation results for the CaM pseudo-ellipse test data.

The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo simulations. The new
frame order representation files have been added to the repository, as well as the intermediate
state files.
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r24666 | bugman | 2014-07-23 08:57:12 +0200 (Wed, 23 Jul 2014) | 8 lines

Updated the frame order optimisation results for the CaM torsionless isotropic cone test data.

The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo simulations. The new
frame order representation files have been added to the repository, as well as the intermediate
state files.
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r24667 | bugman | 2014-07-23 08:58:29 +0200 (Wed, 23 Jul 2014) | 8 lines

Updated the frame order optimisation results for the 2nd CaM pseudo-elliptic cone test data.

The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo simulations. The new
frame order representation files have been added to the repository, as well as the intermediate
state files.
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Merged revisions 24530-24534,24538-24539 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r24530 | bugman | 2014-07-11 16:48:43 +0200 (Fri, 11 Jul 2014) | 7 lines

Sent the verbosity argument to the minfx.grid.grid_split() function for the frame order analysis.

This matches the relax trunk changes for the model-free analysis. The minfx function in the next
release (1.0.8) will now be more verbose, so this will help with user feedback when running the
model-free analysis on a cluster or multi-core system using MPI.
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r24531 | bugman | 2014-07-11 17:21:44 +0200 (Fri, 11 Jul 2014) | 9 lines

Improvements for the parallelised grid search for the frame order analysis.

As each grid point can take wildly different numbers of CPU cycles to calculate the chi-squared
value for, the result of subdividing the grid search was that some subdivisions where incredibly
quick while others required much larger amounts of time. To avoid this bad slave management, the
grid points are now randomised. This means that the subdivisions will require about the same amount
of time to optimise.
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r24532 | bugman | 2014-07-11 17:47:01 +0200 (Fri, 11 Jul 2014) | 10 lines

Moved the setup of the target function data structures in the frame order analysis.

This is for the grid_search and minimise user functions. The target function data setup function
has been renamed to target_fn_data_setup(). This is now called before the Frame_order_grid_command
and Frame_order_minimise_command multi-processor objects are initialised, and all of the data is now
passed into these functions. Although the code is uglier, this has the benefit that the
target_fn_data_setup() function will only be called once. This data setup requires a lot of time,
so for a large cluster, this can be a large time saving for the grid search.
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r24533 | bugman | 2014-07-14 12:17:07 +0200 (Mon, 14 Jul 2014) | 3 lines

Modified the frame_order_free_start.py script to better mimic the frame order auto-analysis.
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r24534 | bugman | 2014-07-15 11:14:39 +0200 (Tue, 15 Jul 2014) | 8 lines

Updated the frame order optimisation results for the 2nd CaM free rotor test data.

The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo simulations. The new
frame order representation files have been added to the repository, as well as the intermediate
state files.
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r24538 | bugman | 2014-07-16 11:32:25 +0200 (Wed, 16 Jul 2014) | 8 lines

Updated the frame order optimisation results for the CaM free rotor test data.

The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo simulations. The new
frame order representation files have been added to the repository, as well as the intermediate
state files.
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r24539 | bugman | 2014-07-16 15:38:08 +0200 (Wed, 16 Jul 2014) | 8 lines

Updated the frame order optimisation results for the CaM missing data free rotor test data.

The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo simulations. The new
frame order representation files have been added to the repository, as well as the intermediate
state files.
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