relax SVN archive

Fix for bug #22505 (https://gna.org/bugs/?22505).

This is the failure of the structure.create_diff_tensor_pdb user function when no structural data is
present. The solution was simple - the CoM of the representation is set to the origin when no
structural data is present, and the check for the presence of data removed.

Merged revisions 25193 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r25193 | bugman | 2014-08-22 09:07:33 +0200 (Fri, 22 Aug 2014) | 14 lines

Fix for the return_r2eff_arrays() dispersion function for exponential curves.

This is a partial solution for bug #22461 (https://gna.org/bugs/?22461).

For the Relax_disp.test_r1rho_kjaergaard_missing_r1 system test, there are multiple relaxation times
for each data set. For example, printing out the exp_type, frq, offset, point, ei, mi, oi, di, and
relax_times data gives:

- R1rho 799777399.1 118.078 431.0 0 0 0 0 [0.0, 0.04, 0.1, 0.2]
- R1rho 799777399.1 118.078 651.2 0 0 0 1 [0.0, 0.04, 0.1, 0.2, 0.4]

Instead of taking the first relaxation time of 0.0, now the maximum time is taken.
........

Created the Structure.test_create_diff_tensor_pdb system test.

This is to show the failure of the structure.create_diff_tensor_pdb user function when no structural
data is present.

Merged revisions 25188-25191 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r25188 | tlinnet | 2014-08-21 19:44:44 +0200 (Thu, 21 Aug 2014) | 10 lines

Inserted intermediate systemtest, to profile R2eff calculation for R1rho.

Systemtest is: Relax_disp.test_bug_9999_slow_r1rho_r2eff_error_with_mc

This systemtest actually fails, if one tries to do a Grid Search.

This is related to the R2eff values stored as dictionary, and
pipe_control.minimise.grid_setup() will fail.

The function 'isNaN(values[i])' cannot handle dictionary.
........
r25189 | tlinnet | 2014-08-21 22:57:45 +0200 (Thu, 21 Aug 2014) | 12 lines

Modified intermediate systemtest:
Relax_disp.test_bug_9999_slow_r1rho_r2eff_error_with_mc

to see if the initial Grid Search for 'i0' and 'R2eff' estimation can be skipped.

This is done by converting the exponential curve, to a linear curve, and calculate
the best parameters by a line of best fit by least squares.

This seems like a promising method as an initial estimator of 'i0' and 'r2eff'.

For 500 to 2000 Monte-Carlo simulations, this could have an influence on the timings,
as all grid searchs could be skipped.
........
r25190 | tlinnet | 2014-08-22 00:37:46 +0200 (Fri, 22 Aug 2014) | 3 lines

Modified systemtest test_bug_9999_slow_r1rho_r2eff_error_with_mc to save data arrays.

This is to prepare a profiling script.
........
r25191 | tlinnet | 2014-08-22 00:37:49 +0200 (Fri, 22 Aug 2014) | 1 line

Added start script with basic data for profiling the relax curve fit.
........

Fix for the return_r2eff_arrays() dispersion function for exponential curves.

This is a partial solution for bug #22461 (https://gna.org/bugs/?22461).

For the Relax_disp.test_r1rho_kjaergaard_missing_r1 system test, there are multiple relaxation times
for each data set. For example, printing out the exp_type, frq, offset, point, ei, mi, oi, di, and
relax_times data gives:

- R1rho 799777399.1 118.078 431.0 0 0 0 0 [0.0, 0.04, 0.1, 0.2]
- R1rho 799777399.1 118.078 651.2 0 0 0 1 [0.0, 0.04, 0.1, 0.2, 0.4]

Instead of taking the first relaxation time of 0.0, now the maximum time is taken.

Added a new redirect for an old relax 2.1 API documentation page.

This is a problem of a capital letter being set to lowercase.

Added start script with basic data for profiling the relax curve fit.

Modified systemtest test_bug_9999_slow_r1rho_r2eff_error_with_mc to save data arrays.

This is to prepare a profiling script.

Modified intermediate systemtest:
Relax_disp.test_bug_9999_slow_r1rho_r2eff_error_with_mc

to see if the initial Grid Search for 'i0' and 'R2eff' estimation can be skipped.

This is done by converting the exponential curve, to a linear curve, and calculate
the best parameters by a line of best fit by least squares.

This seems like a promising method as an initial estimator of 'i0' and 'r2eff'.

For 500 to 2000 Monte-Carlo simulations, this could have an influence on the timings,
as all grid searchs could be skipped.

Inserted intermediate systemtest, to profile R2eff calculation for R1rho.

Systemtest is: Relax_disp.test_bug_9999_slow_r1rho_r2eff_error_with_mc

This systemtest actually fails, if one tries to do a Grid Search.

This is related to the R2eff values stored as dictionary, and
pipe_control.minimise.grid_setup() will fail.

The function 'isNaN(values[i])' cannot handle dictionary.