relax SVN archive

Created an initial Relax_disp.test_lm63_3site_synthetic system test.

This should have been set up a long time ago. It uses the synthetic noise-free data in the
test_suite/shared_data/dispersion/lm63_3site directory which was created for a system test but never
converted into one. The test still needs modifications to allow it to pass.

Moved the cleaning of data points and replacing of values of out loop for model ns mmq 2site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

Fix for systemtest: test_korzhnev_2005_all_data

The masking for replacing values was wrong.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

Speed up for the frame order analyses when only one domain is aligned.

When only one domain is aligned, the reverse Ln3+ to spin vectors for the PCS are no longer
calculated. For most analyses, this should significantly reduce the number of mathematical
operations required for the quasi-random Sobol' point numerical integration.

Changed the parameter values for the Frame_order.test_cam_pseudo_ellipse_torsionless* system tests.

The theta_x and theta_y angles are now swapped. The chi-squared values are now also lower in the
3 system tests as the data is now of much higher precision.

Large increase in precision for the CaM frame order torsionless pseudo-ellipse model test data set.

In addition, the theta_x and theta_y angles have also been swapped so that the new constraint of
0 <= theta_x <= theta_y <= pi built into the analysis is satisfied.

The higher precision is because the number structures in the distribution is now 20 million rather
than 1 million and the numpy.float128 data averaging has been used. The algorithm for finding
suitable random domain positions within the motional limits has been changed as well by extracting
the theta and phi tilt angles from the random rotation, dropping the torsion angle sigma, and
reconstructing the rotation from just the tilt angles. This increases the speed of the data
generation script by minimally 5 orders of magnitude.

Updated documentation on dimensionality of numpy array num_points.

They are in dimension [NE][NS][[NM][NO], where oi gives the number of
dispersion points at that offset.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

Temporary added systemtest: test_korzhnev_2005_all_data_disp_speed_bug.

This makes a minimisation with 1 iteration, and so will give the chi2 value at the preset
parameter values.

This is chi2 value should give 162.5, but gives 74.7104.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

Merged revisions 23881,23945,24008-24009 via svnmerge from
svn+ssh://tlinnet@.../svn/relax/trunk

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r23881 | bugman | 2014-06-12 14:47:31 +0200 (Thu, 12 Jun 2014) | 8 lines

Better handling of the control-C keyboard interrupt signal in the relax test suite.

This includes two changes. The Python 2.7 and higher unittest.installHandler() function is now
called, when present, to terminate all tests using the unittest module control-C handler. The
second change is that the keyboard interrupt signal is caught in a try-except statement, a message
printed out, and the tests terminated. This should be an improvement for all systems.
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r23945 | bugman | 2014-06-13 17:54:50 +0200 (Fri, 13 Jun 2014) | 17 lines

Reverted r23693 as SciPy is actually still used in the frame order analyses.

The command used was:
$ svn merge -r23693:r23692 .

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r23693 | bugman | 2014-06-06 14:24:44 +0200 (Fri, 06 Jun 2014) | 6 lines
Changed paths:
M /trunk/docs/latex/install.tex

Removed all SciPy references in the installation chapter of the manual.

This is because SciPy is no longer used in the frame order analysis, hence it is not used for any
part of relax.
.....
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r24008 | tlinnet | 2014-06-17 09:18:19 +0200 (Tue, 17 Jun 2014) | 1 line

Adding last profiling information for model CR72.
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r24009 | tlinnet | 2014-06-17 09:18:24 +0200 (Tue, 17 Jun 2014) | 8 lines

Added systemtest for model LM63 3 site.

According to results folder in:
test_suite/shared_data/dispersion/Hansen/relax_results/LM63 3-site

This should pass.

But i doesnt?
........

Bug fix for model LM63 3site. The index si has to be used to extract data to lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.