relax SVN archive

Critical fix for the math domain catching of model CR72.

Removed the test for kex >= 1.e5.

This catching should rather be performed on the math functions instead.

Critical fix for the math domain catching of model B14.

This was discovered with the added 8 unit tests demonstrating edge case 'no Rex' failures.

This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

This is to implement catching of math domain errors, before they occur.

When kex is large, ex: kex = 1e5, "nan" values where produced,
which was replaced with 1e100.

The cathing of these occurences needed to be re-written.

Added the 8th unit tests demonstrating edge case 'no Rex' failures of the model 'B14'.

This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

This is to implement catching of math domain errors, before they occur.

These tests cover all parameter value combinations which result in no exchange:

- dw = 0.0,
- pA = 1.0,
- kex = 0.0,
- dw = 0.0 and pA = 1.0,
- dw = 0.0 and kex = 0.0,
- pA = 1.0 and kex = 0.0,
- dw = 0.0, pA = 1.0, and kex = 0.0.
- kex = 1e5,

Critical fix for the math domain catching of model CR72.

This was discovered with the added 8 unit tests demonstrating edge case 'no Rex' failures.

This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

This is to implement catching of math domain errors, before they occur.

When kex is large, ex: kex = 1e5, the values of:
etapos = eta_scale * sqrt(Psi + sqrt_psi2_zeta2) / cpmg_frqs

will exceed possible numerical representation.

The cathing of these occurences needed to be re-written.

Added 8 unit tests demonstrating edge case 'no Rex' failures of the model 'CR72'.

This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

This is to implement catching of math domain errors, before they occur.

These tests cover all parameter value combinations which result in no exchange:

- dw = 0.0,
- pA = 1.0,
- kex = 0.0,
- dw = 0.0 and pA = 1.0,
- dw = 0.0 and kex = 0.0,
- pA = 1.0 and kex = 0.0,
- dw = 0.0, pA = 1.0, and kex = 0.0.
- kex = 1e5,

Merged revisions 23370,23373-23374,23379,23389,23392,23408 via svnmerge from
svn+ssh://tlinnet@.../svn/relax/trunk

........
r23370 | bugman | 2014-05-23 10:18:37 +0200 (Fri, 23 May 2014) | 7 lines

Fix for the Relax_disp.test_cpmg_synthetic_dx_map_points system test.

This uses the default parameter values to start the optimisation, therefore the recent change away
from edge case 'no Rex' values allows the parameter values stored in ds.dx_clust_val to be correctly
optimised.
........
r23373 | bugman | 2014-05-23 11:25:34 +0200 (Fri, 23 May 2014) | 7 lines

Speed up for the version module when using a repository copy of the code.

The repository revision and URL and now stored as module variables, so that the 'svn info' and
'git svn info' commands are only run twice, once for the revision() function and once for the url()
function.
........
r23374 | bugman | 2014-05-23 12:11:36 +0200 (Fri, 23 May 2014) | 15 lines

Large speed up for the relax start up times for svn and git-svn copies of the relax repository.

The 'svn info' and 'git svn info' commands are now only executed once when the version module is
first imported. The revision() and url() functions have been merged into the repo_info() function
and this is called when the module is imported. This repo_info() function stores the repository
revision and URL as the version.repo_revision and version.repo_url module variables. It also
catches if these variables are already set, so that multiple imports of the module do not cause the
repository information to be looked up each time.

Previously the revision() and url() functions where called every time a relax state or result file
was created, hence for repository copies the 'svn info' or 'git svn info' commands were being called
each time. The functions were also called for each interpreter object instantiated, and for each
import of the version module.
........
r23379 | bugman | 2014-05-23 14:45:43 +0200 (Fri, 23 May 2014) | 6 lines

Backported the relax 3.2.1 CHANGES file changes to trunk.

The command used was:
svn merge -r23376:23377 svn+ssh://bugman@.../svn/relax/tags/3.2.1 .
........
r23389 | bugman | 2014-05-23 19:39:53 +0200 (Fri, 23 May 2014) | 6 lines

Small speed up for all the isotropic cone and pseudo-elliptic cone frame order models.

The vector length calculation for the numeric PCS integration has been simplified and shifted
outside of a loop to take advantage of the speed of numpy.
........
r23392 | bugman | 2014-05-24 08:53:35 +0200 (Sat, 24 May 2014) | 3 lines

All three file arguments for the pymol.frame_order user function are now optional.
........
r23408 | bugman | 2014-05-26 09:52:52 +0200 (Mon, 26 May 2014) | 6 lines

Updated all the API documentation links in the dispersion chapter of the manual.

These were pointing to http://www.nmr-relax.com/api/3.1/ whereas they should now be point to
http://www.nmr-relax.com/api/3.2/.
........

Elimination of the error_flag variable from the frame order analysis.

This flag is used to activate some old code paths which have now been deleted as they are never
used.

Fix for the http://www.nmr-relax.com/download.html webpage.

The problem was identified via the W3C markup validation service using the link
http://validator.w3.org/check?uri=http://www.nmr-relax.com/download.html.

Added a redirect for http://www.nmr-relax.com/api/3.1/lib.dispersion.B14-module.html to the website.

This now points to http://www.nmr-relax.com/api/3.2/lib.dispersion.B14-module.html. This is needed
as the API documentation links in the manual were out of date.

Updated all the API documentation links in the dispersion chapter of the manual.

These were pointing to http://www.nmr-relax.com/api/3.1/ whereas they should now be point to
http://www.nmr-relax.com/api/3.2/.