relax SVN archive

Merged revisions 23720 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r23720 | tlinnet | 2014-06-06 22:03:27 +0200 (Fri, 06 Jun 2014) | 5 lines

Modified profiling script, to get closer to the implementation in relax.

An additional test function is setup to figure out how to reshape the numpy arrays in the target function.

bug #22146: (https://gna.org/bugs/?22146) Unpacking of R2A and R2B is performed wrong for clustered "full" dispersion models.
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The lib.compat.norm() replacement function for numpy.linalg.norm() now handles no axis argument.

This is to allow the function to be used in all cases where numpy.linalg.norm() is used, while
providing compatibility with the axis argument and all numpy versions.

Added the full optimisation results for the rotor frame order model.

This is for the 2-site CaM test data using the new frame_order.py optimisation script.

Added the full optimisation results for the free rotor pseudo-ellipse frame order model.

This is for the CaM test data using the new frame_order.py optimisation script.

Fix for the free rotor PDB representation created by the frame_order.pdb_model user function.

The simulation axes were being incorrectly generated from the theta and phi angles, which no longer
exist as they have been replaced by the alpha angle.

Made the logic and comments much clearer about how to reshape, expand axis, and tile numpy arrays.

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

Restored profiling script to normal.

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

Needed to increase the relative tolerance when testing if pA array is 1.

Now system test Relax_disp.test_hansen_cpmg_data_missing_auto_analysis passes.

Also added some comments lines, to prepare for mask replace of values.
For example if only some of etapos values should be replaced.

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

Very important fix, for only replacing part of data array which have Nan values.

Before, all values were replaced, which was wrong.

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

Fixed that arrays are correctly initiated with one or zero values.

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