relax SVN archive

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.

Replaced target function for model IT99, to use higher dimensional numpy array structures.

That makes the model much faster.

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 IT99.

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 IT99, 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.

Documentation is also fixed.

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

Added another timing script for RDC and PCS calculation timings.

This time, the calculation for multiple alignments is now being timed. An addition set of methods
for calculating the values via tensor projections have been added. For 5 alignments and 200
vectors, this demonstrates a potential 20x speed up for this part of the RDC/PCS calculation. Most
of this speed up should be obtainable for the numerical PCS integration in the frame order models.