relax SVN archive

Added simulation support for the RDC and PCS Q factors in the N-state model analysis.

This is for both Monte Carlo and Bootstrap simulation. The simulation RDC and PCS values, as well
as the simulation back calculated values are now stored via the minimise_bc_data() function of
specific_analyses.n_state_model.optimisation in the respective spin or interatomic data containers.
The analysis specific API methods now send the sim_index value into minimise_bc_data(), as well as
the pipe_control.rdc.q_factors() and pipe_control.pcs.q_factors() functions.

Added Monte Carlo and Bootstrap simulation support for the RDC and PCS Q factor calculations.

The pipe_control.rdc.q_factors() and pipe_control.pcs.q_factors() functions have been modified to
support Monte Carlo and Bootstrap simulations. The sim_index argument has been added to allow the Q
factor for the given simulation number to be calculated. All of the Q factor data structures in the
base data pipe now have *_sim equivalents for permanently storing the simulation values. For the
simulation values, all the warnings have been silenced.

Added a missing call to monte_carlo.initial_values in the N_state_model.test_absolute_T system test.

This fixes the commit of r27854, showing that there is not a problem with the Monte Carlo simulations.

Added Monte Carlo simulations to the N_state_model.test_absolute_T system test.

This is to demonstrate a failure of the simulations in certain N-state model setups.

Added 'NMR dynamics' as a meta keyword for all of http://www.nmr-relax.com/ .

Added sample data and analysis script, that will eventually show that there is not much differentce in the sample statistics used for comparing the output of two
very similar datasets.

This is a multiple comparison test with many t tests at once, where the familywise error is controlled by the Holm method.
Even if the values are very equal, and within the standard deviation, this procedure will reject up to 20% of the null hypothesis.

This is not deemed as a suitable method.

Bug #23644 /https://gna.org/bugs/?23644): monte_carlo.error_analysis() does not update the mean value/expectation value from simulations.

Fixes for broken links to my PhD thesis.

Fix committed, where an empty spin placeholder has the select flag set to False.

Bug #23642 (https://gna.org/bugs/index.php?23642): When deleting all spins for a residue, an empty placeholder is where select=True

Added unittest that shows the trickers the bug.

Test added in test_delete_spin_all, and can be accessed with: relax -u _pipe_control.test_spin.

Bug #23642 (https://gna.org/bugs/index.php?23642): When deleting all spins for a residue, an empty placeholder is where select=True

Reverted r27840-r27845, related to Bug #23618, queuing system for multi processors is not well designed.

The changes has not been proven to increase the minimisation time, and some of the fixes introduces unintentional bugs.

The command used was:
svn merge -r27845:r27839 .

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r27840 | tlinnet | 2015-05-27 03:09:48 +0200 (Wed, 27 May 2015) | 3 lines

Adding keyword for verbosity for multi processor mode.

Task #7826 (https://gna.org/task/?7826): Write an python class for the repeated analysis of dispersion data.
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r27841 | tlinnet | 2015-05-27 03:09:50 +0200 (Wed, 27 May 2015) | 2 lines

Adding to user function minimise.execute() the keyword "mp_verbosity", to control the amount
of information to print when running multi processors.
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r27842 | tlinnet | 2015-05-27 03:09:52 +0200 (Wed, 27 May 2015) | 1 line

In multi.processor(), moving up the debugging print-out of running sets of calculatation.
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r27843 | tlinnet | 2015-05-27 03:09:55 +0200 (Wed, 27 May 2015) | 1 line

In pipe_control of minimise, adding the possibility to control verbosity in multi processor mode.
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r27844 | tlinnet | 2015-05-27 03:09:57 +0200 (Wed, 27 May 2015) | 6 lines

Suggestion Fix 1, in multi.processor.run_queue().

This fix changes, that the amount of simulations is not chunked up before sending each chunk to a CPU.
Rather, all jobs are to be submitted after each other, and finished for themselves.

Bug #23618: (https://gna.org/bugs/index.php?23618): queuing system for multi processors is not well designed.
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r27845 | tlinnet | 2015-05-27 03:09:59 +0200 (Wed, 27 May 2015) | 3 lines

Suggestion for fix 2, where jobs are continously replenished when other jobs are finished.

Bug #23618: (https://gna.org/bugs/index.php?23618): queuing system for multi processors is not well designed.
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