relax SVN archive

Methods to replace math domain errors in model ns_cpmg_2site_3d, has been replaced with numpy masks.

number of points has been removed, as the masks utility replaces this.
pB is now moved to be calculated inside. This makes the lib function simpler.
k_AB and k_BA is also now calculated here.
Magnetization vector is also now filled in lib function.

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

Python 3 fix for the CaM frame order system test base script.

Added another timing script for helping with speeding up the frame order analysis.

This is for the part where the rotation matrix for each Sobol' integration point is shifted into the
eigenframe.

Fix for system test Relax_disp.test_cpmg_synthetic_dx_map_points.

By just copying self.back_calc_a to self.back_calc, problem was solved.

In specific_analysis.relax_disp.optimisation in function back_calc_r2eff(), the
function gets the last values stores in the class function.

This is in:
class Disp_result_command(Result_command):
"""Class for processing the dispersion optimisation results.
With:
self.back_calc = back_calc

And back_calc_r2eff() have return model.back_calc

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

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

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

.....
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.
.....

Revert r23692 as SciPy is actually still used in the frame order analyses.

The command used was:
svn merge -r23692:r23691 .

.....
r23692 | bugman | 2014-06-06 14:21:58 +0200 (Fri, 06 Jun 2014) | 5 lines
Changed paths:
M /website/download.html

Removed all references to SciPy on the http://www.nmr-relax.com/download.html webpage.

SciPy is no longer used in the frame order analysis.
.....

Small speed up for all of the frame order models.

The PCS averaging in the quasi-random numerical integration functions now uses the multiply() and
divide() numpy methods to eliminate a loop over the alignments. For this, a new dimension over the
spins was added to the PCS constant calculated in the target function __init__() method. In one
test of the pseudo-ellipse, the time dropped from 191 seconds to 172.

Replaced target function for model ns_cpmg_2site_expanded, to use higher dimensional numpy array structures.

That makes the model much faster.

I cannot get system test: Relax_disp.test_cpmg_synthetic_dx_map_points
to pass.

-------
File "/Users/tlinnet/software/disp_spin_speed/test_suite/system_tests/relax_disp.py", line 1671, in test_cpmg_synthetic_dx_map_points
self.assertEqual(res_file[i], lines[i])
AssertionError: '0.76981 3.9169 0.41353 1\n' != '0.0098838 1.4654 18.661 1\n'
-------

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

Fix for sending in r20 and dw as numpy array in unit tests of ns_cpmg_2site_expanded.

This is after using masks as replacement.

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

Methods to replace math domain errors in model ns_cpmg_2site_expanded, has been replaced with numpy masks.

number of points has been removed, as the masks utility replaces this.
pB is now moved to be calculated inside. This makes the lib function simpler.
k_AB and k_BA is also now calculated here.

Documentation is also fixed.

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