relax SVN archive

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

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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.
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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.
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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.
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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.
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r25301 | bugman | 2014-08-26 17:52:19 +0200 (Tue, 26 Aug 2014) | 3 lines

Removed some printouts accidentally committed in the previous revision.
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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.
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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.
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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.
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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.
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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.
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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.
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Merged revisions 24819-24823,24832-24836 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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

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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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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Merged revisions 24522-24524 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r24522 | bugman | 2014-07-11 10:46:21 +0200 (Fri, 11 Jul 2014) | 12 lines

Parallelised the frame order grid search to run on clusters or multi-core systems via OpenMPI.

This involved the creation of the Frame_order_grid_command class which is the multi-processor
Slave_command for performing the grid search. This was created by duplicating the
Frame_order_minimise_command class and then differentiating both classes.

For the subdivision of the grid search, the new minfx grid.grid_split_array() function is used in
the frame order grid() API method. The grid() method no longer calls the minimise() method but
instead obtains the processor box itself and adds the subdivided grid slaves to the processor. The
relax grid_search user function takes care of the rest.
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r24523 | bugman | 2014-07-11 12:01:20 +0200 (Fri, 11 Jul 2014) | 8 lines

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

A chi-squared value check was added to the Frame_order_result_command.run() method to check if the
value is lower than the current when the result is returned to the master. Without this check, each
grid subdivision result will be stored as they are returned rather than storing the results from the
global minimum of the entire grid search.
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r24524 | bugman | 2014-07-11 15:38:59 +0200 (Fri, 11 Jul 2014) | 7 lines

Added a script for testing out the parameter nesting abilities of the frame order auto-analysis.

This script attempts to find the dynamics solution without knowing where the pivot is located.
Hence this will be as in the auto-analysis were this pivot point will be used as the base for all
other models.
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Merged revisions 24514-24520 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r24514 | bugman | 2014-07-10 18:12:07 +0200 (Thu, 10 Jul 2014) | 5 lines

Changed the minimisation in the frame order system tests where optimisation is activated.

The number of iterations is now set to 1 for speed testing, and the constraints are turned on.
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r24515 | bugman | 2014-07-10 18:13:09 +0200 (Thu, 10 Jul 2014) | 5 lines

Turned on the optimisation flag for the Frame_order.test_cam_free_rotor system test.

This is to activate code paths currently not tested by the test suite.
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r24516 | bugman | 2014-07-10 18:27:10 +0200 (Thu, 10 Jul 2014) | 6 lines

Constraints are now properly turned off in the minimise user function for the frame order analysis.

The A and b matrices from linear_constraints() are now set to None if they are returned as empty
arrays.
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r24517 | bugman | 2014-07-10 19:04:37 +0200 (Thu, 10 Jul 2014) | 26 lines

Parallelised the frame order optimisation code to run on clusters or multi-core systems via OpenMPI.

The optimisation code has been split into the three standard parts of the multi-processor:

- Frame_order_memo is the new Memo object used to store data on the master for use when data is
returned from the slaves.

- Frame_order_minimise_command is the Slave_command which stored all required data for the
optimisation, is pickled and sent to a slave, sets up the target function, and then performs
optimisation.

- Frame_order_result_command is the Result_command initialised by the Slave_command on the slave for
pickling and returning results to the master.

To avoid pickling the target function class, which is not possible, the store_bc_data() and
target_fn_setup() functions of the specific_analyses.frame_order.optimisation module have been
redesigned to work with basic data structures rather than the target function class directly. The
target_fn_setup() function no longer returns an initialised target function class, but rather all
the data assembled prior to the initialisation. And the target function class was itself modified
so that pcs_theta and rdc_theta are always defined to allow the store_bc_data() function to be used
successfully.

This parallelisation currently only allows the Monte Carlo simulations to be run on slave
processors.
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r24518 | bugman | 2014-07-11 09:07:01 +0200 (Fri, 11 Jul 2014) | 21 lines

Reverted r24495 as this is rubbish.

The pivot point needs to be initially guessed to centre the grid search for the pivot to a
reasonable 20 Angstrom box in the PDB space.

The command used was:
svn merge -r24495:r24494 .

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r24495 | bugman | 2014-07-09 15:31:21 +0200 (Wed, 09 Jul 2014) | 7 lines
Changed paths:
M /branches/frame_order_cleanup/specific_analyses/frame_order/parameters.py

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

The pivot parameters are now set to 0.0 if they do not currently exist. They were previously
excluded from this initialisation, but this is required for the frame order models if the pivot is
not initially fixed at a give location in the PDB space.
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r24519 | bugman | 2014-07-11 10:14:45 +0200 (Fri, 11 Jul 2014) | 5 lines

The frame order linear_constraints() function now returns None if no constraints are present.

This allows the code using this to be simplified with respect to turning off the constraints.
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r24520 | bugman | 2014-07-11 10:33:48 +0200 (Fri, 11 Jul 2014) | 6 lines

Improvements for the printout at the start of optimisation of the frame order models.

This is in the target_fn_setup() frame order method. All the printouts are now in one place and
they are now better formatted and better controlled.
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