relax SVN archive

Added target function for the Jacobian of TSMFK01, in target_functions/relax_disp.py.

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

Added partial derivatives for model TSMFK01 and the Jacobian function.

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

Started function estimate_par_err, to estimate errors. All data is collected, and target function initialized.

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

Added initial systemtest Relax_disp.test_task_model_par_est_tsmfk01, to load data, and call back end function for estimating errors for model parameters.

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

Added the simulated data, which will be used for comparison.

This is for 10.000 simulations, since my computer started having problems with 50.000 suimulations.

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

Added initial test data set for TSMK01.
A 50.000 Monte-Carlo simulation will be performed.

For this relax state, all simulated numbers will get extracted to a numpy array and saved with numpy.save.
All spin.PAR_sim attributes will get deleted to save disk space, and the relax state saved again.

In this way, access to all data is granted.

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

Updated the minfx version numbers in the release checklist document.

The version is now 1.0.10, which has not been released yet but will contain the implementation of
the log-barrier constraint algorithm gradient and Hessian.

Merged revisions 25499-25502,25504,25506 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r25499 | bugman | 2014-09-01 14:33:25 +0200 (Mon, 01 Sep 2014) | 8 lines

Modified specific_analyses.relax_disp.parameters.r1_setup() to initialise the 'r1' variable.

This relates to bug 22541 (https://gna.org/bugs/?22541), the R1 fit flag does not work in the GUI.

This is a hack, as all of the dispersion analysis code assumes that all parameters are initialised.
This is a dangerous assumption that will have to be eliminated in the future.
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r25500 | bugman | 2014-09-01 14:37:07 +0200 (Mon, 01 Sep 2014) | 10 lines

The dispersion get_param_values() API method now calls the r1_setup() function.

This relates to bug #22541 (https://gna.org/bugs/?22541), the R1 fit flag does not work in the GUI.

This is to make sure that the parameters are correctly set up prior to obtaining all parameter
values. The R1 parameter is dynamic hence r1_setup() needs to be called at any point model
parameters are accessed, as the R1 parameter can be turned on or off at any time with the
relax_disp.r1_fit user function.
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r25501 | tlinnet | 2014-09-01 14:54:48 +0200 (Mon, 01 Sep 2014) | 1 line

Yet another try to implement constrained method in verify_estimate_r2eff_err_compare_mc.
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r25502 | tlinnet | 2014-09-01 15:09:41 +0200 (Mon, 01 Sep 2014) | 7 lines

Another attempt to reach constrained method in minfx through relax.

I would need to specify:
l: Lower bound constraint vector (l <= x <= u).
u: Upper bound constraint vector (l <= x <= u).
c: User supplied constraint function.
dc: User supplied constraint gradient function.
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r25504 | bugman | 2014-09-01 16:33:30 +0200 (Mon, 01 Sep 2014) | 7 lines

Added a derivation of the R2eff/R1rho error estimate for the two-point measurement to the manual.

This is from http://thread.gmane.org/gmane.science.nmr.relax.devel/6929/focus=6993 and is for the
rate uncertainty of a 2-parameter exponential curve when only two data points have been collected.
The derivation has been added to the dispersion chapter of the manual.
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r25506 | bugman | 2014-09-01 16:40:24 +0200 (Mon, 01 Sep 2014) | 3 lines

Equation fixes for the two-point exponential error derivation in the dispersion chapter of the manual.
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Equation fixes for the two-point exponential error derivation in the dispersion chapter of the manual.

This branch is for developing model parameters errors by writing the Jacobian up for analytical dispersion models.

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