relax SVN archive

Another fix for the minfx version checking in the dep_check module.

The version_comparison() function has been created to perform a proper version number comparison by
stripping trailing zeros, converting the two version numbers to lists of int and comparing the lists
using the Python cmp() function. This will return -1 when the version number is too low, 0 when the
versions are equal, and 1 when the version is higher than the minimum.

Initial try to implement using BFGS, when minimising in bootstrap in systemtest: test_task_model_par_est_tsmfk01.

Results:

50 boot

Simplex, with constraints

param: r2a_err, with err: 0.48131663, compared to MC: 0.49354342, with 50 boot 0.45852174
param: dw_err, with err: 0.30874093, compared to MC: 0.32813703, with 50 boot 0.34714120
param: k_AB_err, with err: 0.64606994, compared to MC: 0.65384783, with 50 boot 0.68158598

Simplex, without constraints

param: r2a_err, with err: 0.48131663, compared to MC: 0.49354342, with 50 boot 0.50583526
param: dw_err, with err: 0.30874093, compared to MC: 0.32813703, with 50 boot 0.30275995
param: k_AB_err, with err: 0.64606994, compared to MC: 0.65384783, with 50 boot 0.64242987

BFGS, with constraints
Cannot compute! Extremely show

BFGS, without constraints
param: r2a_err, with err: 0.48131663, compared to MC: 0.49354342, with 50 boot 0.44000111
param: dw_err, with err: 0.30874093, compared to MC: 0.32813703, with 50 boot 0.00554190
param: k_AB_err, with err: 0.64606994, compared to MC: 0.65384783, with 50 boot 0.69600469

Is there something wrong with scaling again?

task #7824(https://gna.org/task/index.php?7824): Model parameter ERROR estimation from Jacobian and Co-variance matrix of dispersion models.

Fix for dimension extractions, when estimating the parameter errors.

task #7824(https://gna.org/task/index.php?7824): Model parameter ERROR estimation from Jacobian and Co-variance matrix of dispersion models.

Added function to target function to chi2, to try to compute the derivative of the chi2 function.

The function is in a test state, with several tests and looping.

task #7824(https://gna.org/task/index.php?7824): Model parameter ERROR estimation from Jacobian and Co-variance matrix of dispersion models.

Modified systemtest, to minimise with BFGS, but it will fail.

task #7824(https://gna.org/task/index.php?7824): Model parameter ERROR estimation from Jacobian and Co-variance matrix of dispersion models.

Initial try to form the dfunc to be send to minfx.

There will be a problem with dimensionality.

task #7824(https://gna.org/task/index.php?7824): Model parameter ERROR estimation from Jacobian and Co-variance matrix of dispersion models.

Initial try to form the full chi-squared gradient for multiple numpy array axis.

task #7824(https://gna.org/task/index.php?7824): Model parameter ERROR estimation from Jacobian and Co-variance matrix of dispersion models.

Merged revisions 25535 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r25535 | bugman | 2014-09-02 11:24:36 +0200 (Tue, 02 Sep 2014) | 7 lines

Fixes for the Relax_disp.test_estimate_r2eff_err system test.

The kex parameter value checks have all been scaled by 1e-5 to allow for a meaningful floating point
number comparison. The number of significant figures have also been scaled. This allows the test
to now pass on one 64-bit GNU/Linux system.
........

Change to the parameter nesting in the frame order auto-analysis.

The pivot is now taken from the rotor model for all other models. Taking the pivot point from the
isotropic cone model is not a good idea as there are situations where the pivot point optimisation
catastrophically fails, sending the point many tens or hundreds of Angstrom away from the molecule.

The frame order auto-analysis results printout has been extended to include the pivot point.