relax SVN archive

Further improved the profiling of relax curve fit.

This profiling shows, that Python code is about twice as slow as the C code implemented.

But it also shows that optimising with scipy.optimize.leastsq is 20 X faster.
It also gives reasonable error values.

Combining a function for a linear fit to guess the initial values, together
with scipy optimise, will be an extreme time win for estimating R2eff values fast.

A further test would be to use relax Monte-Carlo simulations for say 1000-2000 iterations,
and compare to the errors extracted from estimated covariance.

Further extended the profiling script for curve fitting.

Now profiling is in place for the implemented C code method in relax.

A similar code should now be devised for numpy array for comparing.

But this profiling shows that when contraints=True, is slowing down this procedure by a factor 10 X !

Added Nikolai's original Matlab code to the lib.dispersion.ns_r1rho_2site module docstring.

This is the code taken directly form the original funNumrho.m file, which was the origin of the code
in this module.

Fix for looping over data indices, where tilt_angles has the si index.

bug #22461(https://gna.org/bugs/?22461): NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.

Fix for systemtest not adding spin.isotope to setup information.

bug #22461(https://gna.org/bugs/?22461): NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.

Moved the storing of relax time up before check of missing data in return_r2eff_arrays().

bug #22461(https://gna.org/bugs/?22461): NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.

Merged revisions 25213 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r25213 | bugman | 2014-08-22 14:09:14 +0200 (Fri, 22 Aug 2014) | 7 lines

Improved data checking for all of the Structure system tests.

Before looping over the structural data, the number of lines in the real file and the newly
generated file are compared. This avoids the situation whereby an empty file is produced,
accidentally allowing the test to pass.
........

Modified the Relax_disp.test_r1rho_kjaergaard_missing_r1 system test to pass on 64-bit Linux systems.

The accuracy of the checks of the optimised values have been decreased.

Fix for systemtest Relax_disp.test_exp_fit(), where the spin.isotope was not set.

The new call to return_r2eff_arrays(), when producing graphs, raise RelaxSpinTypeError() if no isotope is set.

bug #22461(https://gna.org/bugs/?22461): NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.

Fix for interpolating time points, when producing xmgrace files for CPMG experiments.

bug #22461(https://gna.org/bugs/?22461): NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.