relax SVN archive

Added two more sections to the frame order chapter of the manual.

This includes a frame order modelling section and PCS numerical integration section. Both are from
a supplement from an in-preparation manuscript.

Fix for the previous commit (r27880).

Most chapters had been commented out and accidentally committed.

Rearrangement of the frame order chapter in the manual.

The theory section has been spun out into its own frame_order_theory.tex LaTeX file for better
organisation.

Added a theory section to the new frame order chapter.

This is taken from an in-preparation supplement.

Created a new skeleton chapter in the relax manual for the frame order analysis.

Merged revisions 27866 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27866 | tlinnet | 2015-07-23 14:08:17 +0200 (Thu, 23 Jul 2015) | 3 lines

Made a summarize function to compare results.

Task #7826 (https://gna.org/task/?7826): Write an python class for the repeated analysis of dispersion data.
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Merged revisions 27854-27865 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27854 | bugman | 2015-06-23 18:14:57 +0200 (Tue, 23 Jun 2015) | 5 lines

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.
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r27855 | bugman | 2015-06-23 18:26:18 +0200 (Tue, 23 Jun 2015) | 5 lines

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.
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r27856 | bugman | 2015-06-24 14:35:32 +0200 (Wed, 24 Jun 2015) | 9 lines

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.
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r27857 | bugman | 2015-06-24 14:39:42 +0200 (Wed, 24 Jun 2015) | 9 lines

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.
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r27858 | bugman | 2015-06-24 14:51:11 +0200 (Wed, 24 Jun 2015) | 3 lines

Removed some accidentally committed debugging printouts.
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r27859 | bugman | 2015-06-25 12:52:26 +0200 (Thu, 25 Jun 2015) | 5 lines

Silenced a warning in the N-state model optimisation if the verbosity is set to zero.

This removes a repetitive warning from the Monte Carlo or Bootstrap simulations.
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r27860 | bugman | 2015-06-25 16:00:59 +0200 (Thu, 25 Jun 2015) | 9 lines

Huge speed up for the Monte Carlo simulations in the N-state model analyses.

This speed up is also for Bootstrap simulations and the frame order analysis. The change affects
the monte_carlo.initial_values user function. The alignment tensor _update_object() method was very
inefficient when updating the Monte Carlo simulation data structures. For each simulation, each of
the alignment tensor data structures were being updated for all simulations. Now only the current
simulations is being updated. This speeds up the user function by many orders of magnitude.
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r27861 | bugman | 2015-06-26 09:56:16 +0200 (Fri, 26 Jun 2015) | 6 lines

Added functions for calculating the geometric mean and standard deviation to the relax library.

These are the geometric_mean() and geometric_std() functions of the lib.statistics module. The
implementation is designed to be fast, using numpy array arithmetic rather than Python loops.
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r27862 | bugman | 2015-06-26 09:57:22 +0200 (Fri, 26 Jun 2015) | 3 lines

Removed some rubbish text from the new lib.statistics.geometric_*() function docstrings.
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r27863 | bugman | 2015-06-26 10:33:34 +0200 (Fri, 26 Jun 2015) | 3 lines

Created a simple unit test for the new lib.statistics.geometric_mean() function.
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r27864 | bugman | 2015-06-26 10:36:14 +0200 (Fri, 26 Jun 2015) | 3 lines

Addition of the file which should have been committed in the last commit (r27863).
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r27865 | bugman | 2015-06-26 10:38:27 +0200 (Fri, 26 Jun 2015) | 3 lines

Added a unit test for the new lib.statistics.geometric_std() function.
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Merged revisions 27852 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27852 | tlinnet | 2015-06-15 23:12:52 +0200 (Mon, 15 Jun 2015) | 9 lines

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.
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Merged revisions 27849-27850 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27849 | tlinnet | 2015-06-13 14:00:39 +0200 (Sat, 13 Jun 2015) | 5 lines

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
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r27850 | tlinnet | 2015-06-13 14:08:44 +0200 (Sat, 13 Jun 2015) | 3 lines

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
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Merged revisions 27848 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27848 | tlinnet | 2015-06-11 13:15:54 +0200 (Thu, 11 Jun 2015) | 45 lines

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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