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Changes
Formatting of exponentials.
* The [[No Rex]] model - the model for no chemical exchange being present.
* The [[LM63]] SQ CPMG-type analytic model - the original Luz and Meiboom 1963 2-site fast exchange equation with parameters {R<sub>2</sub><sup>0</sup>, ..., φ<sub>ex</sub>, k<sub>ex</sub>} [Luz and Meiboom 1963].
* The [[LM63 3-site]] SQ CPMG-type analytic model - the original Luz and Meiboom 1963 3-site fast exchange equation with parameters {R<sub>2</sub><sup>0</sup>, ..., φ<sub>ex,B</sub>, k_Bk<sub>B</sub>, φ<sub>ex,C</sub>, k<sub>C</sub>} [Luz and Meiboom 1963].
* The [[CR72]] SQ CPMG-type analytic model - the reduced Carver and Richards 1972 2-site equation for most time scales whereby the simplification R<sub>2A</sub><sup>0</sup> = R<sub>2B</sub><sup>0</sup> is assumed with the parameters {R<sub>2</sub><sup>0</sup>, ..., p<sub>A</sub>, δω, k<sub>ex</sub>} [Carver and Richards 1972].
* The [[CR72 full]] SQ CPMG-type analytic model - the full Carver and Richards 1972 2-site equation for most time scales with parameters {R<sub>2A</sub><sup>0</sup>, R<sub>2B</sub><sup>0</sup>, ..., p<sub>A</sub>, δω, k<sub>ex</sub>} [Carver and Richards 1972].
* The [[IT99]] SQ CPMG-type analytic model - the Ishima and Torchia 1999 2-site model for all time scales with p<sub>A</sub> ≫ p<sub>B</sub> and with parameters {R<sub>2</sub><sup>0</sup>, ..., φ<sub>ex</sub>, p<sub>A</sub>.δω^<sup>2</sup>, k<sub>ex</sub>} [Ishima and Torchia 1999].
* The [[TSMFK01]] SQ CPMG-type analytic model - the Tollinger et al., 2001 2-site very-slow exchange model for time scales within range of microsecond to second time scale with parameters are {R<sub>2A</sub><sup>0</sup>, ..., δω, k<sub>AB</sub>} [Tollinger et al., 2001].
* The [[NS CPMG 2-site expanded]] SQ CPMG-type numeric model - A model for 2-site exchange expanded using Maple by Nikolai Skrynnikov (Tollinger et al., 2001) with the parameters {R<sub>2</sub><sup>0</sup>, ..., p<sub>A</sub>, δω, k<sub>ex</sub>}.
* Fix for the relaxation dispersion specific _assemble_scaling_matrix() method. The values were all inverted - the matrix should hold values on the same order as the parameter values.
* Fix for the func_exp_fit() relaxation dispersion target function. The parameter index was not correctly calculated.
* The 'exp_fit' relaxation dispersion model now uses the minfx.grid sparseness argument. This is used to skip all parts of the grid search belonging to a different exponential curve or different spin. If the number of curves is N and the number of spins M, the grid size decreases from inc**<sup>(2*N*M) </sup> to (inc**<sup>2</sup>)*N*M. For lots of spins and curves, this is a huge decrease.
* The relaxation dispersion specific _disassemble_param_vector() method is now functional. This should allow the minimise user function to complete.
* Fixes for the dispersion specific _assemble_param_vector() method. The R<sub>2eff</sub> and I<sub>0</sub> spin dictionary structures are now checked for their keys before pulling the value out.
* Added the results for the CR72 model optimisation in CPMGFit using Flemming Hansen's truncated CPMG data.
* Added the CR72 model results to the software comparison document for Hansen's CPMG data.
* Improvements for the φ<sub>ex</sub> and δω relaxation dispersion model parameters. These are now stored with the units of ppm^<sup>2 </sup> and ppm respectively. The conversion to (rad/s)^<sup>2 </sup> and rad/s units respectively now is spin specific, allowing mixed spin types (1H, 13C, 15N, etc.) to be analysed simultaneously.
* Updated the relax results for Hansen's CPMG data for the recent φ<sub>ex</sub> and δω changes.
* Fixes for the CPMGFit results in the software comparison table for Hansen's CPMG data.
* Fix for the relax_disp.sherekhan_input user function. The loop_cluster() function no longer returns spin containers.
* Fix for the r2eff_calc.py script for calculating R<sub>2eff</sub> values from Flemming Hansen's CPMG data.
* Added a check to the dispersion specific minimise() function for the spectrometer field strength. This is essential in all dispersion models to convert between ppm and rad/s units, or ppm^<sup>2 </sup> and (rad/s)^<sup>2 </sup> for the φ<sub>ex</sub> parameter.
* The r1rho_on_res_m61.py dispersion system test script now sets the spectrometer frequency information.
* Removed cdp.model as this makes no sense - a different model can be used per spin cluster. Now the variable cdp.model_type is used to identify the 'R2eff' model. For all other dispersion models this variable is set to 'Disp'.
* Created the IT99 model target function. This is the Ishima and Torchia 1999 2-site model for all timescales with p<sub>A</sub> ≫ p<sub>B</sub>. This commit follows step 4 of the relaxation dispersion model addition tutorial (http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).
* Fix for the lib.dispersion.it99 module. This is the Ishima and Torchia 1999 2-site model for all timescales with p<sub>A</sub> ≫ p<sub>B</sub>. This commit follows step 3 of the relaxation dispersion model addition tutorial (http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).
* Added the support for the p<sub>A</sub>.δω^<sup>2 </sup> parameter 'padw2' to the dispersion specific analysis. This is needed for the Ishima and Torchia 1999 2-site model for all timescales with p<sub>A</sub> ≫ p<sub>B</sub>. This commit follows step 5 of the relaxation dispersion model addition tutorial (http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).
* Added support for the IT99 model to the relax_disp.select_model user function back end. This is the Ishima and Torchia 1999 2-site model for all timescales with p<sub>A</sub> ≫ p<sub>B</sub>. This commit follows step 6 of the relaxation dispersion model addition tutorial (http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).
* Added the support for the t<sub>ex</sub> parameter (t<sub>ex</sub> = 1/(2k<sub>ex</sub>)) to the dispersion specific analysis. This is needed for the Ishima and Torchia 1999 2-site model for all timescales with p<sub>A</sub> ≫ p<sub>B</sub>. This commit follows step 5 of the relaxation dispersion model addition tutorial (http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).
* Added setup function for the system test of KTeilum_FMPoulsen_MAkke_2006 data. Progress sr #3071: https://gna.org/support/?3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax.
* Fixed a spelling mistake in a number of file names. This is for the test suite data located at test_suite/shared_data/dispersion/KTeilum_FMPoulsen_MAkke_2006.
* Fixes for the units in the dispersion parameter table in the user manual. The units for δω are rad.s^<sup>-1 </sup> when used in the equations, but it is stored internally as ppm.
* Truncated the dataset to only one residue L61. The truncated dataset will be expanded later. Progress sr #3071: https://gna.org/support/?3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax.
* Modified the script file for saving of a truncated base_pipe state file. Progress sr #3071: https://gna.org/support/?3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax.
* Added the button for the interatom.define user function in preparation for the MQ dispersion data. This is in the dispersion tab of the GUI.
* The return_cpmg_frqs() and return_spin_lock_nu1() functions now return numpy arrays. These are functions from specific_analyses.relax_disp.disp_data.
* Speed ups for the optimisation of all of the R<sub>1ρ</sub> dispersion models. The spin-lock field strength data structure is now converted from Hz to rad.s^<sup>-1 </sup> in the dispersion target function initialisation. Previously the conversion was happening multiple times per target function call. This has a noticeable effect on the test suite timings.
* Some small speed ups for the TP02 R<sub>1ρ</sub> dispersion model optimisation. Some unneeded calculations and aliases were removed.
* Added the write-out of 'δω' and 'k<sub>AB</sub>' for model TSMFK01, when performing auto-analysis. Progress sr #3071: https://gna.org/support/?3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax.
* Shifted the optimisation printouts for the dispersion analysis out of the memo. This improved the ordering of the printed out messages when running on a cluster. Instead of having multiple optimisation printouts followed by a list of the corresponding optimised values, now they are interleaved as they should be.
* Changed the definition of t<sub>ex</sub> thanks to feedback from Nikolai Skrynnikov. This was previously defined as t<sub>ex</sub> = 1/(2k<sub>ex</sub>) to be compatible with CPMGFit, but has now been changed to t<sub>ex</sub> = 1/k<sub>ex</sub>.
* Converted the 'IT99' dispersion model parameters to p<sub>A</sub> and δω. This is thanks to feedback from Nikolai Skrynnikov. I have no idea why the φ<sub>ex</sub> and p<sub>A</sub>.δω^<sup>2 </sup> parameters were being used in the first place. The model results after the change are identical.
* Fix for the optimised parameter printout - the parameters are now scaled. This problem was only recently introduced.
* The dispersion sample scripts now have the NUMERIC_ONLY boolean variable defined.