relax SVN archive

Implemented the shifting to the average position for the frame_order.simulate user function backend.

This simply sends the structural object into the new average_position() function of the
specific_analyses.frame_order.geometric module.

Spun out the code for shifting to the average frame order position into a new function.

The old code of the create_ave_pos() of the specific_analyses.frame_order.geometric module has been
shifted into the new average_position() function. This will allow the code to be reused by other
parts of relax to obtain the average frame order structures.

Huge speed up for the Frame_order.test_auto_analysis user function.

The pseudo-Brownian dynamics simulation via the frame_order.simulate user function has been
massively speed up to allow the test to be almost as fast as before.

Added new arguments to the frame order auto-analysis for the frame_order.simulate user function.

These are the brownian_step_size, brownian_snapshot and brownian_total arguments which are passed
directly into the frame_order.simulate user function. This gives the user more control, as well as
allowing the test suite to speed up this part of the analysis.

Decreased the time required for the Frame_order.test_cam_* system tests.

The frame_order.simulate user function now only creates a total of 20 snapshots rather than 1000.

Created the backend framework for the frame_order.simulate user function.

The backend specific_analyses.frame_order.uf.simulate() function performs all data checks required,
prepares the output file object, assembles the frame order parameter values and pivot point, and
creates a copy of the structural object object with the ensemble collapsed into a single model.

All this data is then passed into the new lib.frame_order.simulation.brownian() function. This
initialises all required data structures and the structural object. The main loop of the simulation
is also implemented, taking snapshots at every fixed number of steps and terminating the loop once
the total number of snapshots are reached. The snapshot consists of copying the original unrotated
structural model and rotating it into the new position. The rotation is currently the identity
matrix.

The old specific_analyses.frame_order.geometric.create_distribution() stub function has been
deleted.

Created a basic text based progress meter in the new lib.text.progress module.

This is taken from the script test_suite/shared_data/frame_order/cam/generate_base.py.

Merged revisions 25942-25945 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r25942 | bugman | 2014-09-22 09:59:35 +0200 (Mon, 22 Sep 2014) | 6 lines

Created the Structure.test_collapse_ensemble system test.

This is used to test a planned feature of the internal structural object. The collapse_ensemble()
method will be created to remove all but one model in the structural ensemble.
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r25943 | bugman | 2014-09-22 10:14:25 +0200 (Mon, 22 Sep 2014) | 5 lines

Fixes for the structure.add_atom user function to allow for list of lists for the atomic position.

This allows different coordinates to be supplied for each model.
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r25944 | bugman | 2014-09-22 10:16:35 +0200 (Mon, 22 Sep 2014) | 5 lines

Modified the Structure.test_collapse_ensemble system test to check the initial values.

This is for sanity reasons as the test coverage of the structure.add_atom user function is poor.
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r25945 | bugman | 2014-09-22 10:29:55 +0200 (Mon, 22 Sep 2014) | 5 lines

Implemented the internal structural object collapse_ensemble() method.

This allows the Structure.test_collapse_ensemble system test to pass.
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Implemented the internal structural object collapse_ensemble() method.

This allows the Structure.test_collapse_ensemble system test to pass.

Modified the Structure.test_collapse_ensemble system test to check the initial values.

This is for sanity reasons as the test coverage of the structure.add_atom user function is poor.