Changes

* The [[DPL94]] R_1ρ-type analytic model - the Davis et al., 1994 2-site fast exchange equation extending the '[[M61' ]] model for off-resonance data with parameters {R_1ρ', ..., φ_ex, k_ex} [Davis et al., 1994].

* Started to redesign how R_2eff is handled in the relaxation dispersion analysis. Instead of being part of the optimisation of the dispersion model, it will itself be the model named '[[R2eff' ]] (converted from the 'exp_fit' model). This model will either use the calc user function to determine R_2eff when the fixed relaxation period experiment is selected, or fit exponential curves using the relax_fit C module for the variable relaxation period experiments. The R_2eff values will then be copied over for each dispersion model in the auto-analysis using the value.copy user function.

* The [[R2eff ]] model now works for the variable time relaxation period and exponential curve-fitting.

* Elimination of the relax_disp.calc_r2eff user function. This user function, which is non-functional anyway, is not needed. The calculation of the R_2eff values will occur with the optimisation of the '[[R2eff' ]] model (with a call to the calc user function for the fixed time period experiment types) so direct calculation through a specific user function is not needed.

* The Relax_disp.test_hansen_cpmg_data_fast_2site system test now uses the [[R2eff ]] model. The equivalent slow exchange system test also uses the model. This model will be used to find the R_2eff values from the fixed relaxation time period data.

* Changed the φ_ex parameter in the [[LM63 ]] model back to rex.

* Converted all of the specific_analyses.relax_disp.parameters module to handle different models. The R_2eff and I₀ parameters are now only part of the '[[R2eff' ]] model and all other standard parameters belong to all of the other models.

* Updates to the relaxation dispersion auto-analysis. The Grace plots created are now more dependent on the current model, so that dispersion curves are only created for the '[[R2eff' ]] model. The specific_analyses.relax_disp.variables module is now also being used.

* Shifted the [[LM63 ]] dispersion model functions into the new lib.dispersion.lm63 module.

* Started to add support for Monte Carlo simulations for the relaxation dispersion models. This is for all models except '[[R2eff']]. The changes are extensive but incomplete. The new functions disp_point_key_from_index() and disp_point_index_from_key() have been added to the specific_analyses.relax_disp.disp_data module, but the disp_point_index_from_key() function still needs work. The _back_calc() method of the specific_analyses.relax_disp.Relax_disp class has been redesigned, as well as base_data_loop() method and all methods which depend on it.* Updated the relaxation dispersion system tests of the Hansen CPMG data for the new models. The models are now '[[LM63' ]] and '[[CR72']], and the tests have been renamed to Relax_disp.test_hansen_cpmg_data_LM63 and Relax_disp.test_hansen_cpmg_data_CR72.

* Fix for the linear constraints setup of the '[[R2eff' ]] relaxation dispersion model. There are no constraints, so the specific_analyses.relax_disp.parameters.linear_constraints() function now returns A and b values of None.

* A number of fixes to partly enable Monte Carlo simulations for the non '[[R2eff' ]] dispersion models.

* Fixes for the [[LM63 ]] dispersion CPMG model. The 'r2' model parameter is now an array as there is one R₂ value per magnetic field strength. And the 'rex' parameter has been renamed to 'φ_ex' and is scaled quadratically with the field strength within the optimisation target function.

* Created the Relax_disp.test_hansen_cpmgfit_input system test. This is for checking the operation of the relax_disp.cpmgfit_input user function conversion of Flemming Hansen's CPMG R_2eff values into input files for CPMGFit. A relax state file containing the results of an analysis of an '[[R2eff' ]] model analysis of the truncated data has been added to the test suite data to speed up the test and to check the loading of dispersion state files.

* Fix for the [[LM63 ]] dispersion model target function - the scaled φ_ex value is now used for the R₂.* Fixes for the relaxation dispersion auto-analysis for the [[LM63 ]] model. The Rex parameter is now the φ_ex parameter.

* Added a file which compares the results for the [[LM63 ]] model with Hansen's CPMG data between all programs. This currently includes relax, NESSY and CPMGFit.

* Fix for the linear constraints for the '[[R2eff' ]] model. The A and b matrices are no longer set to None, as this kills the auto-analysis or any analysis when constraints are turned on. Now the constraints 0 ≤ R_2eff ≤ 200 and I₀ ≥ 0 are used.

* Updated the [[LM63 ]] model comparison table.

* Fix for the dispersion auto-analysis write_results() method. The i0 parameter text file and 2D Grace file are now only produced for the '[[R2eff' ]] model with the exponential curve base data types.* Simplified the Relax_disp.test_hansen_trunc_data GUI test. The '[[CR72' ]] model is now deactivated and the grid search sized decreased from the default of 21 to 4.

* Updated the relax_disp.select_model user function frontend for the [[CR72 ]] dispersion model. This includes fixing the parameter list and the equations presented to the user.

* Added the [[CR72 ]] model equations to the relax library. This is for the Carver and Richards 1972 2-site exchange model covering all time scales.* Initial implementation of the [[CR72 ]] target function.

* Fixes to the specific_analyses.relax_disp modules to add support for the [[CR72 ]] dispersion model. The parameters for the [[CR72 ]] model are now both correct and correctly handled.* Fix for the spin container list of parameters for the [[CR72 ]] model.* The [[CR72 ]] dispersion model equations are now more robust against math domain errors. This is for the trigonometric functions which cannot handle certain input values.

* Added the initial results of the [[CR72 ]] model in relax for Flemming Hansen's truncated CPMG data.

* Added support for the '[[CR72' ]] or 'Full_CPMG' model to the relax_disp.cpmgfit_input user function.* 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.

* Fix for the [[CR72 ]] model equation in lib.dispersion.cr72.r2eff_CR72(). The eta scaling factor was incorrect.* Updated the relax results for the truncated CPMG data from Flemming Hansen. This is for the recent fixes of the [[CR72 ]] model equations. Now relax produces identical results to ShereKhan for the [[LM63 ]] and [[CR72 ]] models.

* Added the relax results for the '[[No Rex' ]] model.

* Added the new '[[M61' ]] model to the specific_analyses.relax_disp.variables module. This is the Meiboom 1961 model for 2-site fast exchange for R_1ρ-type experiments.* Added the [[M61 ]] model to the relax_disp.select_model user function frontend. This is the Meiboom 1961 model for 2-site fast exchange for R_1ρ-type experiments.* Added the [[M61 ]] model equations to the relax library. This is for the Meiboom 1961 2-site fast exchange model for R_1ρ-type experiments.* Created the [[M61 ]] 2-site fast exchange dispersion model target function. This is for the Meiboom 1961 model for 2-site fast exchange for R_1ρ-type experiments. The code for the func_M61() method was copied without modification from the func_LM63() method.

* Added support for the [[M61 ]] model to the relax_disp.select_model user function back end. This is for the Meiboom 1961 2-site fast exchange model for R_1ρ-type experiments.

* Model selection in the dispersion auto-analysis is only performed if 2 or more models are present. Excluding the '[[R2eff' ]] model, if only 0 or 1 models are optimised, then model selection is skipped and a warning is given. This avoids tracebacks in the model_selection user function.

* Expanded the synthetic on-resonance R_1ρ test suite data. The data now consists of a full set of dispersion curves for the [[M61 ]] model.

* Fix for the [[M61 ]] model target function. The spin-lock fields need to be used, not the CPMG frequencies.* Created the Relax_disp.test_r1rho_on_res_fixed_time_m61 system test. This checks the R_1ρ-type experiment with a fixed relaxation time period using the '[[R2eff' ]] and '[[M61' ]] models. It uses the auto-analysis for this, and the 'r1rho_on_res' synthetic relaxation data.

* Added the '[[No Rex' ]] model to the relax script for optimising Flemming Hansen's CPMG data.

* 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'.

* Added the '[[M61 skew' ]] model to the specific_analyses.relax_disp.variables module. This is the Meiboom 1961 model for skewed populations (p_A ≫ p_B). This commit follows step 1 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added the '[[M61 skew' ]] model to the relax_disp.select_model user function frontend. This is the Meiboom 1961 model for skewed populations (p_A ≫ p_B). This commit follows step 2 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].

* Added the [[M61 skew ]] model equations to the relax library. This is the Meiboom 1961 on-resonance 2-site model for skewed populations (p_A ≫ p_B). This commit follows step 3 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Created the [[M61 skew ]] model target function. This is the Meiboom 1961 on-resonance 2-site model for skewed populations (p_A ≫ p_B). This commit follows step 4 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].

* Added support for the [[M61 skew ]] model to the relax_disp.select_model user function back end. This is the Meiboom 1961 on-resonance 2-site model for skewed populations (p_A ≫ p_B). This commit follows step 6 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].

* Created test data for the '[[M61 skew' ]] R_1ρ model. This is the Meiboom 1961 on-resonance 2-site model for skewed populations (p_A ≫ p_B). This commit follows step 7 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].

* Increased the precision of the hansen_data.py relaxation dispersion system test script. This actually speeds up the test, as the Monte Carlo simulations are significantly speed up when the [[CR72 ]] model optimises to the solution.

* Fixes for the grid search for the '[[M61 skew' ]] dispersion model. The p_A parameter search is now between 0.85 and 1.

* Added the '[[DPL94' ]] model to the specific_analyses.relax_disp.variables module. This is the David, Perlman and London 1994 R_1ρ 2-site fast exchange model. This commit follows step 1 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added the '[[DPL94' ]] model to the relax_disp.select_model user function frontend. This is the David, Perlman and London 1994 R_1ρ 2-site fast exchange model. This commit follows step 2 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].

* Added the [[DPL94 ]] model equations to the relax library. This is the David, Perlman and London 1994 R_1ρ 2-site fast exchange model. This commit follows step 3 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Created the [[DPL94 ]] model target function. This is the David, Perlman and London 1994 R_1ρ 2-site fast exchange model. This commit follows step 4 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added support for the [[DPL94 ]] model to the relax_disp.select_model user function back end. This is the David, Perlman and London 1994 R_1ρ 2-site fast exchange model. This commit follows step 6 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].

* Added the '[[IT99' ]] model to the specific_analyses.relax_disp.variables module. This is the Ishima and Torchia 1999 2-site model for all timescales with p_A ≫ p_B. This commit follows step 1 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added the '[[IT99' ]] model to the relax_disp.select_model user function frontend. This is the Ishima and Torchia 1999 2-site model for all timescales with p_A ≫ p_B. This commit follows step 2 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Updated the model lists of the dispersion analyses GUI element. This adds the [[IT99 ]] CPMG-type model and the [[DPL94 ]] and M61B [[M61b]] R_1ρ-type models.* Fixes for the [[IT99 ]] model description in the relax_disp.select_model user function. This is the Ishima and Torchia 1999 2-site model for all timescales with p_A ≫ p_B. This commit follows step 2 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added the [[IT99 ]] model equations to the relax library. This is the Ishima and Torchia 1999 2-site model for all timescales with p_A ≫ p_B. This commit follows step 3 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].

* Created the [[IT99 ]] model target function. This is the Ishima and Torchia 1999 2-site model for all timescales with p_A ≫ p_B. This commit follows step 4 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].

* 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_A ≫ p_B. This commit follows step 6 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].

* Added support for the [[IT99 ]] model to the relax_disp.cpmgfit_input user function. This is the Ishima and Torchia 1999 2-site model for all timescales with p_A ≫ p_B.

* Fix for the [[LM63 ]] model for the relax_disp.cpmgfit_input user function. The grid search was incorrectly set up - the parameter is Tau, not t_ex.* Fixes for the [[IT99 ]] model for the relax_disp.cpmgfit_input user function.* Changed the CPMGFit grid search options for the [[IT99 ]] model in the relax_disp.cpmgfit_input user function.* Fix for the setup of the relaxation dispersion target functions for the [[IT99 ]] model.* Added the relax optimisation results for the [[IT99 ]] model applied to Flemming Hansen's CPMG data.

* Added the [[IT99 ]] model to the software comparison table for Hansen's CPMG data. This includes only the results from relax (and possibly not fully debugged results at that).

* Updated the CPMGFit results for the [[IT99 ]] model using Flemming Hansen's CPMG data.

* Updated the relax results for Flemming Hansen's CPMG data for the [[IT99 ]] model fixes.* Fixes for the relax_disp.cpmgfit_input user function for the [[IT99 ]] model grid search options.* Updated the CPMGFit results for the [[IT99 ]] grid search fixes of the last commit.

* Disabled the Relax_disp.test_r1rho_on_res_fixed_time_m61b system test as the '[[M61b' ]] model is rubbish. The model cannot be properly optimised as the parameters are not independent of each other.

* Fix for the dispersion auto-analysis - p_A and p_B parameters are no longer output for the [[IT99 ]] model. These are not parameters of this model.

* Added the '[[NS CPMG 2-site star' |NS 2-site star]] model to the specific_analyses.relax_disp.variables module. This is the model of the numerical solution for the 2-site Bloch-McConnell equations using complex conjugate matrices. This commit follows step 1 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].

* Added the '[[NS CPMG 2-site star' |NS 2-site star]] model to the relax_disp.select_model user function frontend. This is the model of the numerical solution for the 2-site Bloch-McConnell equations using complex conjugate matrices. This commit follows step 2 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].

* Created the '[[NS CPMG 2-site star|NS 2-site star' ]] model target function. This is the model of the numerical solution for the 2-site Bloch-McConnell equations using complex conjugate matrices. This commit follows step 4 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added support for the R_2B⁰ parameter as required by the '[[NS CPMG 2-site star' |NS 2-site star]] model. This is the model of the numerical solution for the 2-site Bloch-McConnell equations using complex conjugate matrices. This commit follows step 5 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added support for the '[[NS CPMG 2-site star' |NS 2-site star]] model to the relax_disp.select_model user function back end. This is the model of the numerical solution for the 2-site Bloch-McConnell equations using complex conjugate matrices. This commit follows step 6 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].

* Added parameter conversions to go from p_A and k_ex to k_ge and k_eg. This is for the '[[NS CPMG 2-site star' |NS 2-site star]] numerical model. The conversions have been added to the start of the target function to minimise mathematical operations to speed up the code.

* The fixed relaxation time period is now sent into the '[[NS CPMG 2-site star' |NS 2-site star]] dispersion model.

* The '[[NS CPMG 2-site star' |NS 2-site star]] model is now more robust against math domain failures. This includes the failure of the logarithmic of zero matrices.* Speed ups of the '[[NS CPMG 2-site star|NS 2-site star' ]] dispersion model optimisation. The relaxation and magnitisation data structures are now initialised with the target function initialisation, rather than being created at each target function call. The Rex and M0 matrices are now updated at the base of the target function rather than in the lib.dispersion.ns_2site_star module to minimise the number of mathematical operations per target function call. And the M0 matrix has changed shape and a dot product is used in lib.dispersion.ns_2site_star to create Moft instead.

* More speed ups of the '[[NS CPMG 2-site star' |NS 2-site star]] dispersion model. A number of calculations have been shifted to the target function initialisation code, avoiding unnecessary repetitive mathematical operations.* Improvement of the error handling in the '[[NS CPMG 2-site star|NS 2-site star' ]] model. The fA and p_B parameters are no longer being checked. Instead a Mgx value of 0.0 is being checked for. This catches additional problems. And now instead of the R_2eff value being set to zero, it is set to 1e99. This is because log of zero is -inf, and then multiplied by a negative constant gives positive inf.

* Reworked the dispersion chapter of the manual for the recent support of numerical models. This includes better sectioning and section labelling and referencing, and the addition of the '[[NS CPMG 2-site star' |NS 2-site star]] numerical model. The model and parameter tables have been updated as well.* Added the '[[NS CPMG 2-site star|NS 2-site star red' ]] model to the specific_analyses.relax_disp.variables module. This is the model of the numerical solution for the 2-site Bloch-McConnell equations using complex conjugate matrices, whereby the simplification R_2A⁰ = R_2B⁰ is assumed. This commit follows step 1 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].

* Added the '[[NS CPMG 2-site star|NS 2-site star red' ]] model to the relax_disp.select_model user function frontend. This is the model of the numerical solution for the 2-site Bloch-McConnell equations using complex conjugate matrices, whereby the simplification R_2A⁰ = R_2B⁰ is assumed. This commit follows step 2 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].

* Created the '[[NS CPMG 2-site star|NS 2-site star red' ]] model target function. This is the model of the numerical solution for the 2-site Bloch-McConnell equations using complex conjugate matrices, whereby the simplification R_2A⁰ = R_2B⁰ is assumed. The code in common with the '[[NS CPMG 2-site star' |NS 2-site star]] model has been shifted into the new calc_ns_2site_star_chi2() method. This commit follows step 4 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added support for the '[[NS CPMG 2-site star|NS 2-site star red' ]] model to the relax_disp.select_model user function back end. This is the model of the numerical solution for the 2-site Bloch-McConnell equations using complex conjugate matrices, whereby the simplification R_2A⁰ = R_2B⁰ is assumed. This commit follows step 6 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added the '[[NS CPMG 2-site star|NS 2-site star red' ]] model to the relax user manual. This is the model of the numerical solution for the 2-site Bloch-McConnell equations using complex conjugate matrices, whereby the simplification R_2A⁰ = R_2B⁰ is assumed. This commit follows step 2 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].

* Added the '[[CR72|CR72 red' ]] model to the specific_analyses.relax_disp.variables module. This is the Carver and Richards 1972 analytic model with the simplification R_2A⁰ = R_2B⁰. The current '[[CR72' full|CR72]] makes the same assumption, but that model will be expanded to support R_2A⁰ and R_2B⁰ later. This commit follows step 1 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added the '[[CR72|CR72 red' ]] model to the relax_disp.select_model user function frontend. This is the Carver and Richards 1972 analytic model with the simplification R_2A⁰ = R_2B⁰. The current '[[CR72' full|CR72]] makes the same assumption, but that model will be expanded to support R_2A⁰ and R_2B⁰ later. This commit follows step 2 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Created the '[[CR72|CR72 red' ]] model target function. This is the Carver and Richards 1972 analytic model with the simplification R_2A⁰ = R_2B⁰. The current '[[CR72' full|CR72]] makes the same assumption, but that model will be expanded to support R_2A⁰ and R_2B⁰ later. The code in common with the [[CR72 full|CR72]] model has been shifted into the new calc_CR72_chi2() method. This commit follows step 4 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added support for the '[[CR72|CR72 red' ]] model to the relax_disp.select_model user function back end. This is the Carver and Richards 1972 analytic model with the simplification R_2A⁰ = R_2B⁰. The current '[[CR72' full|CR72]] makes the same assumption, but that model will be expanded to support R_2A⁰ and R_2B⁰ later. This commit follows step 6 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added the '[[CR72|CR72 red' ]] model to the relax user manual. This is the Carver and Richards 1972 analytic model with the simplification R_2A⁰ = R_2B⁰. The current '[[CR72' full|CR72]] makes the same assumption, but that model will be expanded to support R_2A⁰ and R_2B⁰ later. This commit follows step 2 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* LaTeX improvements for the '[[NS CPMG 2-site star|NS 2-site star red ]] model' section of the dispersion chapter of the manual.* Expanded the [[CR72 full|CR72]] model to handle both the R_2A⁰ and R_2B⁰ parameters. The '[[CR72|CR72 red' ]] model now functions as the old [[CR72 full|CR72 ]] model where R_2A⁰ = R_2B⁰ = R₂⁰. All parts of the code have been modified. The lib.dispersion.cr72.r2eff_CR72() function has been expanded to support the full Carver and Richards 1972 equations, dropping back to the simplified form if R_2A⁰ = R_2B⁰.

* Fix for the Relax_disp.test_hansen_cpmg_data_auto_analysis system test for model name change. This is for the change from the '[[CR72' ]] model to '[[CR72|CR72 red' ]] model.* Added the '[[NS CPMG 2-site 3D|NS 2-site' ]] model to the specific_analyses.relax_disp.variables module. This is the model of the numerical solution for the 2-site Bloch-McConnell equations. It originates as optimization function number 1 from the fitting_main_kex.py script from Mathilde Lescanne, [https://gna.org/users/pasa Paul Schanda], and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://gna.org/task/?7712#comment2 and https://gna.org/support/download.php?file_id=18262). This commit follows step 1 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added the '[[NS CPMG 2-site 3D|NS 2-site' ]] model to the relax_disp.select_model user function frontend. This is the model of the numerical solution for the 2-site Bloch-McConnell equations. It originates as optimization function number 1 from the fitting_main_kex.py script from Mathilde Lescanne, [https://gna.org/users/pasa Paul Schanda], and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://gna.org/task/?7712#comment2 and https://gna.org/support/download.php?file_id=18262). This commit follows step 2 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added the '[[NS CPMG 2-site 3D|NS 2-site' ]] R_2eff calculating function to the relax library. This is the model of the numerical solution for the 2-site Bloch-McConnell equations. It originates as optimization function number 1 from the fitting_main_kex.py script from Mathilde Lescanne, [https://gna.org/users/pasa Paul Schanda], and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://gna.org/task/?7712#comment2 and https://gna.org/support/download.php?file_id=18262). This commit follows step 3 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].

* Created the '[[NS CPMG 2-site 3D|NS 2-site' ]] model target function. This is the model of the numerical solution for the 2-site Bloch-McConnell equations. It originates as optimization function number 1 from the fitting_main_kex.py script from Mathilde Lescanne, [https://gna.org/users/pasa Paul Schanda], and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://gna.org/task/?7712#comment2 and https://gna.org/support/download.php?file_id=18262). This commit follows step 4 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Converted the '[[NS CPMG 2-site' 3D|NS 2-site]] model to '[[NS CPMG 2-site 3D' |NS 2-site 3D]] to be more specific. This might change again in the future.* Added support for the '[[NS CPMG 2-site 3D|NS 2-site 3D' ]] model to the relax_disp.select_model user function back end. This is the model of the numerical solution for the 2-site Bloch-McConnell equations. It originates as optimization function number 1 from the fitting_main_kex.py script from Mathilde Lescanne, [https://gna.org/users/pasa Paul Schanda], and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://gna.org/task/?7712#comment2 and https://gna.org/support/download.php?file_id=18262). This commit follows step 6 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Lots of fixes for the relaxation dispersion target function module for the '[[NS CPMG 2-site 3D' |NS 2-site 3D]] model.

* Speed ups for the '[[NS CPMG 2-site 3D' |NS 2-site 3D]] model. The pi-pulse propagator is created only once upon target function initialisation rather than for each function call, each spin cluster, each magnetic field strength, each dispersion point, and each CPMG block.

* Added the '[[NS CPMG 2-site 3D|NS 2-site 3D red' ]] model to the specific_analyses.relax_disp.variables module. This is the '[[NS CPMG 2-site 3D' |NS 2-site 3D]] model with R_2A⁰ = R_2B⁰ = R₂⁰. This commit follows step 1 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added the '[[NS CPMG 2-site 3D|NS 2-site 3D red' ]] model to the relax_disp.select_model user function frontend. This is the '[[NS CPMG 2-site 3D|NS 2-site 3D' ]] model with R_2A⁰ = R_2B⁰ = R₂⁰. This commit follows step 2 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Created the '[[NS CPMG 2-site 3D|NS 2-site 3D red' ]] model target function. This is the '[[NS CPMG 2-site 3D' |NS 2-site 3D]] model with R_2A⁰ = R_2B⁰ = R₂⁰. This commit follows step 4 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added support for the '[[NS CPMG 2-site 3D|NS 2-site 3D red' ]] model to the relax_disp.select_model user function back end. This is the '[[NS CPMG 2-site 3D' |NS 2-site 3D]] model with R_2A⁰ = R_2B⁰ = R₂⁰. This commit follows step 6 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Updated all of the numerical model sections of the dispersion chapter of the manual. This includes additions for the '[[NS CPMG 2-site 3D' |NS 2-site 3D]] and '[[NS CPMG 2-site 3D|NS 2-site 3D red' ]] models.* Updated the '[[NS CPMG 2-site 3D' |NS 2-site 3D]] and '[[NS CPMG 2-site 3D|NS 2-site 3D red' ]] models in the dispersion chapter of the relax manual. The models are now included in the tables and in the introduction.

* Added the '[[NS CPMG 2-site expanded|NS 2-site expanded' ]] model to the specific_analyses.relax_disp.variables module. This is the numerical model for the 2-site Bloch-McConnell equations expanded using Maple by Nikolai Skrynnikov. This commit follows step 1 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added the '[[NS CPMG 2-site expanded' |NS 2-site expanded]] model to the relax_disp.select_model user function frontend. This is the numerical model for the 2-site Bloch-McConnell equations expanded using Maple by Nikolai Skrynnikov. This commit follows step 2 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added the '[[NS CPMG 2-site expanded' |NS 2-site expanded]] R_2eff calculating function to the relax library. This is the numerical model for the 2-site Bloch-McConnell equations expanded using Maple by Nikolai Skrynnikov. It originates as optimization function number 5 from the fitting_main_kex.py script from Mathilde Lescanne, [https://gna.org/users/pasa Paul Schanda], and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://gna.org/task/?7712#comment2 and https://gna.org/support/download.php?file_id=18262). This commit follows step 3 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].

* Created the '[[NS CPMG 2-site expanded' |NS 2-site expanded]] model target function. This is the numerical model for the 2-site Bloch-McConnell equations expanded using Maple by Nikolai Skrynnikov. It originates as optimization function number 5 from the fitting_main_kex.py script from Mathilde Lescanne, [https://gna.org/users/pasa Paul Schanda], and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://gna.org/task/?7712#comment2 and https://gna.org/support/download.php?file_id=18262). This commit follows step 4 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added support for the '[[NS CPMG 2-site expanded' |NS 2-site expanded]] model to the relax_disp.select_model user function back end. This is the numerical model for the 2-site Bloch-McConnell equations expanded using Maple by Nikolai Skrynnikov. It originates as optimization function number 5 from the fitting_main_kex.py script from Mathilde Lescanne, Paul Schanda][https://gna.org/users/pasa , and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://gna.org/task/?7712#comment2 and https://gna.org/support/download.php?file_id=18262). This commit follows step 6 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Fix for the relax_disp.select_model user function for the '[[NS CPMG 2-site expanded' |NS 2-site expanded]] model. There is only one R₂⁰ parameter as R_2A⁰ = R_2B⁰ in this model.* Added the '[[NS CPMG 2-site expanded' |NS 2-site expanded]] model to the relax user manual. This is the numerical model for the 2-site Bloch-McConnell equations expanded using Maple by Nikolai Skrynnikov. It originates as optimization function number 5 from the fitting_main_kex.py script from Mathilde Lescanne, [https://gna.org/users/pasa Paul Schanda], and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://gna.org/task/?7712#comment2 and https://gna.org/support/download.php?file_id=18262). This commit follows step 2 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].

* Import fix for the '[[NS CPMG 2-site expanded' |NS 2-site expanded]] dispersion model target function.

* Created the Relax_disp.test_hansen_cpmg_data_CR72_full system test for checking the '[[CR72 full' ]] model.

* Created the Relax_disp.test_hansen_cpmg_data_ns_2site_3D system test. This checks the '[[NS CPMG 2-site 3D|NS 2-site 3D' ]] numerical dispersion model against some truncated CPMG data from Flemming Hansen.* Created the Relax_disp.test_hansen_cpmg_data_ns_2site_3D_full system test. This checks the '[[NS CPMG 2-site 3D full|NS 2-site 3D full' ]] numerical dispersion model against some truncated CPMG data from Flemming Hansen. The parameter checks have not been updated as there appears to be a bug.* Created system tests for the rest of the numerical dispersion models. These include Relax_disp.test_hansen_cpmg_data_ns_2site_expanded, Relax_disp.test_hansen_cpmg_data_ns_2site_star and Relax_disp.test_hansen_cpmg_data_ns_2site_star_full. This checks the '[[NS CPMG 2-site expanded|NS 2-site expanded']], '[[NS CPMG 2-site star|NS 2-site star']], and '[[NS CPMG 2-site star full|NS 2-site star full' ]] numerical dispersion models against some truncated CPMG data from Flemming Hansen. The parameter checks have not been updated for the '[[NS CPMG 2-site expanded|NS 2-site expanded' ]] and '[[NS CPMG 2-site star full|NS 2-site star full' ]] models as there appears to be bugs.* Fixes for the Relax_disp.test_hansen_cpmg_data_auto_analysis system test. The checks for the '[[CR72|CR72 red' ]] model are now against the '[[CR72 full|CR72' ]] model. And the models optimised only now include '[[No Rex']], '[[LM63']], '[[CR72']], and '[[IT99']], massively speeding up the test.

* Updated the model lists for the relax scripts for optimising Flemming Hansen's CPMG data. The model lists now include the numeric models and the '[[CR72 full' ]] model.

* Added the '[[LM63 3-site' ]] model to the specific_analyses.relax_disp.variables module. This is the Luz and Meiboom 1963 analytic model for three exchanging sites. This commit follows step 1 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added the '[[LM63 3-site' ]] model to the relax_disp.select_model user function frontend. This is the Luz and Meiboom 1963 analytic model for three exchanging sites. This commit follows step 2 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added the '[[LM63 3-site' ]] model to relaxation dispersion chapter of the relax user manual. This is the Luz and Meiboom 1963 analytic model for three exchanging sites. This commit follows step 2 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added the '[[LM63 3-site' ]] R_2eff calculating function to the relax library. This is the Luz and Meiboom 1963 analytic model for three exchanging sites. This commit follows step 3 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Fixes for the '[[LM63 3-site' ]] model equations in the relaxation dispersion chapter of the user manual.* Created the '[[LM63 3-site' ]] model target function. This is the Luz and Meiboom 1963 analytic model for three exchanging sites. This commit follows step 4 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added support to the relaxation dispersion analysis for the '[[LM63 3-site' ]] model parameters. This is the Luz and Meiboom 1963 analytic model for three exchanging sites. This commit follows step 3 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added support for the '[[LM63 3-site' ]] model to the relax_disp.select_model user function back end. This is the Luz and Meiboom 1963 analytic model for three exchanging sites. This commit follows step 6 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added support for the '[[LM63 3-site' ]] parameters to the specific_analyses.relax_disp.parameters module. This is the Luz and Meiboom 1963 analytic model for three exchanging sites. This commit follows step 5 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added the '[[LM63 3-site' ]] model to the dispersion scripts for Flemming Hansen's CPMG data.

* Some fixes for the '[[LM63 3-site' ]] dispersion model. The library code was not accepting the correct arguments and it was referencing a non-existent parameter, and the grid search setup was failing.* Added support for optimising the '[[LM63 3-site' ]] dispersion model with Art Palmer's CPMGFit. This is for the relax_disp.cpmgfit_input user function. This model in CPMGFit is called '3-site_CPMG'.

* Updated the CPMGFit results for the '[[LM63 3-site' ]] model. This is for the truncated CPMG data from Flemming Hansen.* Speed ups for the '[[LM63 3-site' ]] target function. Some mathematical operations have been shifted from the library code into the target function so that is only calculates once per function call.* Updated the relax results for Flemming Hansen's truncated CPMG data for the '[[LM63 3-site' ]] model.* The dispersion auto-analysis now outputs files for the k_B, kC, φ_ex,B, and φ_ex,C parameters. This is in the write_results() method and is for creating text files and Grace plots for the 'LM [[LM63 3-site' ]] model.* Created some synthetic test data for the '[[LM63 3-site' ]] dispersion model. This will be used to test CPMGFit and relax's implementations.* Updated the '[[LM63 3-site' ]] dispersion model test data. The CPMG frequencies are now more realistic.* Removed the old Sparky peak lists for the '[[LM63 3-site' ]] dispersion model test data.* Added the new Sparky peak lists for the '[[LM63 3-site' ]] dispersion model test data.* Updated the reference Sparky peak lists for the '[[LM63 3-site' ]] dispersion model test data.

* Added scripts for calculating the R_2eff values for the '[[LM63 3-site' ]] dispersion model test data.

* Fix for the dispersion auto-analysis for when only the single [[R2eff ]] model is optimised. This is for the case of exponential curve fitting, and allows Monte Carlo simulations to proceed even when the mc_sim_all_models flag is False.

* Made the '[[LM63 3-site' ]] dispersion model test data more realistic. Previously all the rates were within a few decimal places of the R₂⁰ values. Now the dispersion is much more significant.* Modified the '[[LM63 3-site' ]] dispersion model test data again. This time the data has been changed to be that of two residues rather than two spins.* Another update of the '[[LM63 3-site' ]] dispersion model test data. This data now makes CPMGFit happy.* Added the CPMGFit results for the '[[LM63 3-site' ]] dispersion model test data.* Added the relax results for the '[[LM63 3-site' ]] dispersion model test data.* Added a warning not to use the '[[LM63 3-site' ]] model to the dispersion chapter of the user manual.* Added the '[[LM63 3-site' ]] dispersion model to the model list in the GUI. It is not selected by default.

* Fix for the model equivalence setup in the nesting() method of the dispersion auto-analysis. This is the use of the analytic [[CR72 ]] model parameters for the numeric models to avoid the grid search.

* Updated the relax results for Flemming Hansen's truncated CPMG data. This includes the '[[CR72 full' ]] model and all the numeric models (excluding the *full models).

* Reactivated Monte Carlo simulations for the '[[R2eff' ]] model for exponential data curves. This is within the optimise() method of the dispersion auto-analysis.

* Added the '[[TP02' ]] model to the specific_analyses.relax_disp.variables module. This is the Trott and Palmer 2002 R_1ρ analytic model for 2-site exchange. This commit follows step 1 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added the '[[TP02' ]] model to the relax_disp.select_model user function frontend. This is the Trott and Palmer 2002 R_1ρ analytic model for 2-site exchange. This commit follows step 2 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added the '[[TP02' ]] model to relaxation dispersion chapter of the relax user manual. This is the Trott and Palmer 2002 R_1ρ analytic model for 2-site exchange. This commit follows step 2 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added the '[[TP02' ]] R_1ρ' calculating function to the relax library. This is the Trott and Palmer 2002 R_1ρ analytic model for 2-site exchange. This commit follows step 3 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial]. The Matlab code from Skrynnikov and Tollinger has not been converted to Python code yet. This is to allow the Matlab->Python conversion to be followed.* Fix for the '[[M61 skew' ]] dispersion model indexing in the user manual.* Added the '[[NS CPMG 2-site expanded|NS 2-site expanded' ]] model to the CPMG dispersion sample script.* Added the '[[NS CPMG 2-site expanded|NS 2-site expanded' ]] and '[[TP02' ]] models to the script in the manual. This is in the script section of the dispersion chapter of the user manual.

* Fixes for the [[TP02 ]] model section of the dispersion chapter of the manual.* Created the '[[TP02' ]] model target function. This is the Trott and Palmer 2002 R_1ρ analytic model for 2-site exchange. This commit follows step 4 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added support for the '[[TP02' ]] model to the relax_disp.select_model user function back end. This is the Trott and Palmer 2002 R_1ρ analytic model for 2-site exchange. This commit follows step 6 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* The spectrometer frequency information is now checked for the [[TP02 ]] model.* Started to create a script to create synthetic data for the [[TP02 ]] dispersion model. This still needs a lot of work.

* Created the synthetic data for the [[TP02 ]] dispersion model. The Sparky peak lists have been created and added to the repository.* Modified the synthetic data for the [[TP02 ]] dispersion model. The data is more closely mimics that from the paper, and should now be in the slow exchange regime.* Updated the [[M61 ]] R_1ρ model conditions in the table in the user manual.* Updated the [[TP02 ]] R_1ρ model conditions in the table in the manual. This cannot be fast exchange.

* Added the new '[[TSMFK01' ]] model to the specific_analyses\relax_disp\variables.py module. This is the Tollinger/Kay model for the 2-site very-slow exchange model for CPMG-type experiments, which cover the range of microsecond to second time scale. Paper by M. Tollinger, N.R. Skrynnikov, F.A.A. Mulder, J.D.F. Kay and L.E. Kay (2001). 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.* lib/dispersion/lm63.py is copied to tsmfk01.py as part of the implementation of the [[TSMFK01 ]] model equation. 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 [[TSMFK01 ]] model to the user_functions/relax_disp.py select_model user function frontend. 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.* Created the [[TSMFK01 ]] model target function for 2-site very-slow exchange model, range of microsecond to second time scale. 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 [[TSMFK01 ]] model equations to the relax library lib/dispersion/tsmfk01.py. 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.* The chemical shift of each spin is now taken into account for the synthetic data for the [[TP02 ]] dispersion model. The data now properly reflects the spin lock offset.

* Changed the synthetic data file names for the [[TP02 ]] dispersion model.

* Added support for the [[TSMFK01 ]] model to the relax_disp.select_model user function back end. 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.

* The [[TP02 ]] model code is now in a semi functional state. The lib.dispersion code has been fixed to properly handle the data it receives and the target function code has been updated to pass in the correct data.* The [[TP02 ]] model R_1ρ off-resonance test data creation script now creates files of the R₁ relaxation data. These files are needed for the system tests, as R₁ data needs to be read.

* Fix for the synthetic data for the [[TP02 ]] dispersion model. The nitrogen chemical shift was not converted from ppm to rad/s before being used to calculate the offsets.

* Fix for the [[TP02 ]] dispersion model. The rotating frame tilt angle for this model is calculated from the population averaged chemical shift and not the equal weighted average.

* Fix for the synthetic data for the [[TP02 ]] dispersion model. The chemical shift is being set to that of state A, the major species, rather than the non-weighted chemical shift average. This could also have been set to the population weighted average.* The [[TP02 ]] dispersion model now assumes the chemical shift is that of the major population A. Previously the linear chemical shift average was assumed.

* Fixes for the [[DPL94 ]] model to make it truly off-resonance. The tilt angles and R₁ data are now used by the target function.

* Added the '[[NS R1rho 2-site' ]] model to the specific_analyses.relax_disp.variables module. This is the numerical model for the 2-site Bloch-McConnell equations for R_1ρ data. This commit follows step 1 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added the '[[NS R1rho 2-site' ]] model to the relax_disp.select_model user function frontend. This is the numerical model for the 2-site Bloch-McConnell equations for R_1ρ data. This commit follows step 2 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added the '[[NS R1rho 2-site' ]] R_1ρ calculating function to the relax library. This is the numerical model for the 2-site Bloch-McConnell equations for R_1ρ data. This code originates from the Skrynikov & Tollinger code (the sim_all.tar file https://gna.org/support/download.php?file_id=18404 attached to https://gna.org/task/?7712#comment5). Specifically the funNumrho.m file. This commit follows step 3 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].

* Created the '[[NS R1rho 2-site' ]] model target function. This is the numerical model for the 2-site Bloch-McConnell equations for R_1ρ data. The code originates from the funNumrho.m file from the Skrynikov & Tollinger code (the sim_all.tar file https://gna.org/support/download.php?file_id=18404 attached to https://gna.org/task/?7712#comment5). This commit follows step 4 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added support for the '[[NS R1rho 2-site' ]] model to the relax_disp.select_model user function back end. This is the numerical model for the 2-site Bloch-McConnell equations for R_1ρ data. The code originates from the funNumrho.m file from the Skrynikov & Tollinger code (the sim_all.tar file https://gna.org/support/download.php?file_id=18404 attached to https://gna.org/task/?7712#comment5). This commit follows step 6 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added the '[[NS R1rho 2-site' ]] model to the relax user manual. This is the numerical model for the 2-site Bloch-McConnell equations for R_1ρ data. The code originates from the funNumrho.m file from the Skrynikov & Tollinger code (the sim_all.tar file https://gna.org/support/download.php?file_id=18404 attached to https://gna.org/task/?7712#comment5). This commit follows step 2 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].

* Created a save file for the r1rho_off_res_tp02 dispersion data optimised to the [[R2eff ]] model. This will be used for faster system tests.* Created the Relax_disp.test_r1rho_ns_r1rho_2site_to_tp02 system test for the new '[[NS R1rho 2-site' ]] model. This tests the '[[NS R1rho 2-site' ]] model against the R_1ρ off-resonance test data from the '[[TP02' ]] model.* A number of fixes for the '[[NS R1rho 2-site' ]] dispersion model. The model should now be fully functional. The chemical shift and R₁ related data are now assembled for this model, and the data correctly passed from the target function to the lib.dispersion module.* The Relax_disp.test_r1rho_ns_r1rho_2site_to_tp02 system test now passes. The optimised values have been hard-coded into the system test. They do not match the [[TP02 ]] results, but are close.

* Added the '[[TP02' ]] and '[[NS R1rho 2-site' ]] models to the R_1ρ model list in the dispersion GUI. These models were missing from the list.* Fix for the '[[NS R1rho 2-site' ]] model description in the relax_disp.select_model user function.* The relax_disp.select_model GUI wizard combo element now uses Unicode for the dispersion parameters. This is for all the models. The '[[LM63 3-site' ]] model parameter list has also been fixed to match the current set.

* Added the '[[NS R1rho 2-site' ]] model to the dispersion auto-analysis.* Added the '[[TP02' ]] model to the dispersion auto-analysis.

* Added the first system test for model [[CR72 ]] for the kteilum_fmpoulsen_makke_cpmg_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.

* Added "[[CR72 full]]" test suite for kteilum_fmpoulsen_makke_cpmg_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.

* Started a system test for model [[TSMFK01]]. 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.

* Fix for the model list in the GUI - the [[TSMFK01 ]] model entry was broken.

* Some small speed ups for the [[TP02 ]] R_1ρ dispersion model optimisation. Some unneeded calculations and aliases were removed.* Added the write-out of 'δω' and 'k_AB' 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.* Added to calculate the tau_cpmg times when model is [[TSMFK01]]. 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 desc. item for model [[TSMFK01]]. 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 [[TSMFK01 ]] to model overview table. 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 subsection with [[TSMFK01 ]] model. 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.* Fix for adding [[TSMFK01 ]] to sample scripts. 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 Tollinger model [[TSMFK01 ]] to sample scripts. 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 Remco Sprangers' truncated ClpP data to test_suite/shared_data/dispersion/Spranger_ClpP. This is the data attached to https://gna.org/task/?7712#comment6, and it will be used for testing the implementation of the '[[NS MMQ 2-site|MQ NS 2-site' ]] model, when added to relax.

* Created a relax script for analysing Remco Sprangers' ClpP data with the '[[NS MMQ 2-site|MQ NS 2-site' ]] model. This currently does not work, as the model is absent.

* Updated the relax script for analysing Remco Sprangers' ClpP data with the '[[NS MMQ 2-site|MQ NS 2-site' ]] model. The error analysis has been removed as it is identical to what the auto-analysis does.

* Created the Relax_disp.test_sprangers_cpmg_data_auto_analysis system test. This checks the '[[NS MMQ 2-site|MQ NS 2-site' ]] model against Remco Sprangers' MQ CPMG data using the auto-analysis.* Fixes for the checks of the new Relax_disp.test_sprangers_cpmg_data_auto_analysis system test. The '[[NS MMQ 2-site|MQ NS 2-site' ]] model checks were still set up to those of the Relax_disp.test_hansen_cpmg_data_auto_analysis system test.* Added the '[[NS MMQ 2-site|MQ NQ NS CPMG 2-site' ]] model to the dispersion variables. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Adding_the_model_to_the_list The new dispersion variable MODEL_MQ_NS_CPMG_2SITE has been added. As this is a new data type, multi-quantum CPMG, the new MODEL_LIST_MQ_CPMG and MODEL_LIST_MQ_CPMG_FULL lists have been created.

* Created the lib.text.gui.dwH Unicode string for use with the '[[NS MMQ 2-site|MQ NS 2-site' ]] dispersion model.* Added the '[[NS MMQ 2-site|MQ NS CPMG 2-site' ]] model to the relax_disp.select_model user function frontend. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_disp.select_model_user_function_front_end Two new sections were added to the user function docstring for the MQ CPMG and MQ R_1ρ experiment types.* Added support for the '[[NS MMQ 2-site|MQ NS CPMG 2-site' ]] model to the relax_disp.select_model user function back end. This is the numeric solution for 2-site exchange for multi-quantum CPMG-type data. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_disp.select_model_user_function_back_end.* Added support for the new 'δω_H' dispersion parameter. This is needed for the '[[NS MMQ 2-site|MQ NS CPMG 2-site' ]] model support. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Adding_support_for_the_parameters.

* Added the multi-quantum CPMG and R_1ρ experiment types to the dispersion variables. This is needed for the '[[NS MMQ 2-site|MQ NS CPMG 2-site' ]] model. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Creating_a_new_experiment_type.

* Added support for the MQ dispersion data type to the specific_analyses.relax_disp.disp_data module. This is needed for the '[[NS MMQ 2-site|MQ NS CPMG 2-site' ]] model. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Creating_a_new_experiment_type.* Added support for the MQ dispersion data types to the rest of relax. This is needed for the '[[NS MMQ 2-site|MQ NS CPMG 2-site' ]] model, and the changes affect the dispersion data checks and the dispersion target functions. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Creating_a_new_experiment_type.

* Updated the relax_disp.exp_type user function for the new 'MQ CPMG' and 'MQ R1rho' experiment types. This is needed for the '[[NS MMQ 2-site|MQ NS CPMG 2-site' ]] model. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Creating_a_new_experiment_type.* Created the '[[NS MMQ 2-site|MQ NS CPMG 2-site' ]] model target function. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_target_function.* Added the '[[NS MMQ 2-site|MQ NS CPMG 2-site' ]] R_1ρ calculating function to the relax library. This is the 2-site numeric solution for multi-quantum CPMG-type data. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_library.* Updated the '[[NS MMQ 2-site|MQ NS CPMG 2-site' ]] model target function to match the function in the relax library.

* Added the '[[NS MMQ 2-site|MQ NS CPMG 2-site' ]] model to the dispersion auto-analysis. This is the 2-site numeric solution for multi-quantum CPMG-type data. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_auto-analysis.* Added the '[[NS MMQ 2-site|MQ NS CPMG 2-site' ]] model to the GUI model list. This is the 2-site numeric solution for multi-quantum CPMG-type data. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_GUI.

* Fixed the '[[NS MMQ 2-site|MQ NS CPMG 2-site' ]] model description in the relax_disp.select_model user function. The magnitisation vector is 2D, not 3D.

* Added the '[[NS MMQ 2-site|MQ NS CPMG 2-site' ]] model to the relax user manual. This is the 2-site numeric solution for multi-quantum CPMG-type data. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_manual.* Simplified the '[[NS MMQ 2-site|MQ NS CPMG 2-site' ]] model code in lib.dispersion.* Fixes for the '[[NS MMQ 2-site|MQ NS CPMG 2-site' ]] model equations in the user manual.

* Added a script and results files for the base '[[R2eff' ]] model for Remco Sprangers' ClpP data.

* Converted the Relax_disp.test_sprangers_cpmg_data_auto_analysis system test to not use the auto-analysis. The test has been renamed to Relax_disp.test_sprangers_data_to_mq_ns_cpmg_2site. The optimisation is now for the cluster and has been severely cut back. The '[[NS MMQ 2-site|MQ NS CPMG 2-site' ]] model appears to be rubbish anyway - it looks to be indeterminate with multiple solutions, and possibly infinite lines of solutions. The test now passes, and quickly.* Created the Relax_disp.test_sprangers_data_to_mq_cr72 system test. This was copied from the Relax_disp.test_sprangers_data_to_mq_ns_cpmg_2site system test and the model changed to '[[MQ CR72']]. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_test_suite.* Added the '[[MQ CR72' ]] model to the dispersion variables. This is the Carver and Richards (1972) 2-site model expanded for MQ CPMG data by Korzhnev et al., 2004. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Adding_the_model_to_the_list.* Added the '[[MQ CR72' ]] model to the relax_disp.select_model user function frontend. This is the Carver and Richards (1972) 2-site model expanded for MQ CPMG data by Korzhnev et al., 2004. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_disp.select_model_user_function_front_end.* Added support for the '[[MQ CR72' ]] model to the relax_disp.select_model user function back end. This is the Carver and Richards (1972) 2-site model expanded for MQ CPMG data by Korzhnev et al., 2004. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_disp.select_model_user_function_back_end.* Created the '[[NS MMQ 2-site|MQ NS CPMG 2-site' ]] model target function. This is the Carver and Richards (1972) 2-site model expanded for MQ CPMG data by Korzhnev et al., 2004. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_target_function.* Added the '[[MQ CR72' ]] R_2eff calculating function to the relax library. This is the Carver and Richards (1972) 2-site model expanded for MQ CPMG data by Korzhnev et al., 2004. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_library. The corresponding target function was updated to input the correct arguments.* Added the '[[MQ CR72' ]] model to the dispersion auto-analysis. This is the Carver and Richards (1972) 2-site model expanded for MQ CPMG data by Korzhnev et al., 2004. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_auto-analysis.* Added the '[[MQ CR72' ]] model to the GUI model list. This is the Carver and Richards (1972) 2-site model expanded for MQ CPMG data by Korzhnev et al., 2004. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_GUI.

* Added a relax script for the '[[MQ CR72' ]] model optimised using Flemming Hansen's CPMG data. This is to demonstrate, though not exactly successfully, that the '[[MQ CR72' ]] model can collapse to the '[[CR72' ]] model. The imperfection might be due to truncation artefacts in the sin ratio in the mD and mZ factors. The results files and output log file from the script have been added to the repository as well.* Updates for the script and results for the '[[MQ CR72' ]] model optimised using Flemming Hansen's CPMG data.* Added a script and results files for optimising Sprangers' ClpP MQ CPMG data to the '[[MQ CR72' ]] model.

* Added a script and results files for optimising Sprangers' ClpP MQ CPMG data to the '[[MQ CR72' ]] model. This is with all spins clustered. It complements the files which are used for the pre-run results of the auto-analysis.

* Added the Tollinger et al., 2001 reference for the '[[NS CPMG 2-site expanded' ]] model. This reference was communicated in a private email.

* Modified the relaxation dispersion auto-analysis to take nesting of MQ models. This is specifically the nesting of the analytic '[[MQ CR72' ]] model and the '[[NS MMQ 2-site|MQ NS CPMG 2-site' ]] models. The analytic solution is now used as the optimisation starting point for the numeric model.

* Added scripts and results for optimising Sprangers' ClpP MQ CPMG data to the '[[NS MMQ 2-site|MQ NS CPMG 2-site' ]] model. This includes two scripts for non-clustered followed by clustered analysis using the '[[MQ CR72' ]] model in the auto-analysis so its parameters will be used as the optimisation starting point for the '[[NS MMQ 2-site|MQ NS CPMG 2-site' ]] model. The results files for both scripts have been added to the repository.* Added the '[[MQ CR72' ]] model to the relax user manual. This is the Carver and Richards (1972) 2-site model expanded for MQ CPMG data by Korzhnev et al., 2004. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_manual.

* Completed the Relax_disp.test_hansen_cpmg_data_auto_analysis_numeric system test. This now checks all the optimised parameter values and makes sure that no '[[CR72' ]] model was selected.

* Fixes for the calc user function for the dispersion analysis. This now does something logical for the non-[[R2eff ]] models. The chi-squared value is now being calculated and stored. Previously this was only calculating the R_2eff/R_1ρ values for fixed relaxation time period data for the '[[R2eff' ]] model and failing for all others. Now the pre-existing _back_calc_r2eff() method is used to back-calculate and store the chi-squared value.

* Shifted the '[[NS CPMG 2-site expanded' ]] model to the top of the CPMG numerical solutions in the manual. This is because this is the default model which should be used in most cases.* A 20-25% speed increase for the '[[NS CPMG 2-site expanded' ]] dispersion model. Many repetitive mathematical operations have been eliminated and the equations have been changed to optimise the calculation speed.

* Added all of the equations for the '[[NS CPMG 2-site expanded' ]] dispersion model to the relax manual. These are essentially the source code modified to look good in LaTeX.* Fix for the '[[NS CPMG 2-site expanded' ]] model equations in the manual.

* Bug fix for the '[[NS MMQ 2-site|MQ NS CPMG 2-site' ]] model. This was found with the aid of private feedback from Dmitry Korzhnev and him emailing his cpmg_fitd9 program. The problem is that he defines the 'n' parameter as half of a CPMG block. The code was however assuming that 'n' is a full CPMG block.

* Started the conversion of the '[[NS MMQ 2-site|MQ NS CPMG 2-site' ]] model to '[[MMQ 2-site']]. This follows from the post at http://article.gmane.org/gmane.science.nmr.relax.devel/4734.* Renamed all of the '[[NS MMQ 2-site|MQ NS CPMG 2-site' ]] modules and functions for the change to '[[MMQ 2-site']]. This follows from the post at http://article.gmane.org/gmane.science.nmr.relax.devel/4734.* Added the ZQ and DQ CPMG experiment types to the dispersion variables. This is needed for the '[[NS MMQ 2-site|MQ NS CPMG 2-site' ]] model change to '[[MMQ 2-site' ]] and follows from the post at http://article.gmane.org/gmane.science.nmr.relax.devel/4734. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Creating_a_new_experiment_type.

* Added support for the ZQ and DQ CPMG data type to the specific_analyses.relax_disp.disp_data module. This is needed for the '[[NS MMQ 2-site|MQ NS CPMG 2-site' ]] model change to '[[MMQ 2-site' ]] and follows from the post at http://article.gmane.org/gmane.science.nmr.relax.devel/4734. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Creating_a_new_experiment_type.* Completed the support for ZQ and DQ CPMG experiment types in relax. This is needed for the '[[NS MMQ 2-site|MQ NS CPMG 2-site' ]] model change to '[[MMQ 2-site' ]] and follows from the post at http://article.gmane.org/gmane.science.nmr.relax.devel/4734. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Creating_a_new_experiment_type.* The '[[MMQ 2-site' ]] model target function can now handle multiple CPMG data types.

* Turned off the δω, δω_H > 0 constraint for the '[[MMQ 2-site' ]] model.

* Proper handling of the back-calculated dispersion data for the new '[[MMQ 2-site' ]] model.

* Converted the '[[IT99' ]] dispersion model parameters to p_A and δω. This is thanks to feedback from Nikolai Skrynnikov. I have no idea why the φ_ex and p_A.δω² parameters were being used in the first place. The model results after the change are identical.

* Updated the text and Grace files output for the '[[IT99' ]] model in the dispersion auto-analysis.

* Improvements for the relax_disp.insignificance user function. Text is now printed out when a spin is deselected. And all spins set to the '[[R2eff' ]] model are skipped.* The relaxation dispersion auto-analysis now accepts the 'insignificance' argument. This is then used in the relax_disp.insignificance user function prior to the optimisation of each model, so that spins with insignificant dispersion curves are not optimised. The '[[R2eff' ]] and '[[No Rex' ]] models are skipped for obvious reasons.

* Added the '[[No Rex' ]] model to the R1rho_analysis.py sample script.

* The error analysis is now skipped in the dispersion auto-analysis if the '[[R2eff' ]] model is not given. It is then assumed that R_2eff/R_1ρ data has already been loaded into the base data pipe and hence the error analysis is not needed. This avoids fatal errors.

* Fix for the Relax_disp.test_hansen_cpmg_data_auto_analysis_numeric system test for 32-bit Linux. The '[[NS CPMG 2-site expanded' ]] model checks have been turned off again for residue 71 as these results are far to variable.

* Added the TP04 [[TP02]] and [[MP05 ]] R_1ρ dispersion models to the manual. These are not implemented in relax, or any of the software in the software comparison section, but are included for completeness. This was pointed out by Art Palmer.

* Added the [[TAP03 ]] model to the dispersion chapter of the user manual.

* Added the '[[MP05' ]] model to the dispersion variables. This is the Miloushev and Palmer 2005 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Adding_the_model_to_the_list.* Added the '[[MP05' ]] model to the relax_disp.select_model user function frontend. This is the Miloushev and Palmer 2005 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_disp.select_model_user_function_front_end.* Added support for the '[[MP05' ]] model to the relax_disp.select_model user function back end. This is the Miloushev and Palmer 2005 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_disp.select_model_user_function_back_end.* Created the '[[MP05' ]] model target function. This is the Miloushev and Palmer 2005 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_target_function.* Added the '[[MP05' ]] R_2eff calculating function to the relax library. This is the Miloushev and Palmer 2005 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_library. Just in case git-svn does not preserve the file copying history, the lib/dispersion/mp05.py file was copied from the tp02.py file.* Debugging of the '[[MP05' ]] dispersion model - optimisation is now setup correctly. This is the Miloushev and Palmer 2005 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax.html#Debugging.* Fixes and improvements to the Relax_disp.test_tp02_data_to_mp05 system test. The [[MP05 ]] model values, which are almost the same as the [[TP02 ]] model parameters, are now being checked. The optimised parameters are now being printed out to aid in debugging. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax.html#Debugging.

* Added the '[[MP05' ]] model to the GUI model list. This is the Miloushev and Palmer 2005 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_GUI.* Added the '[[MP05' ]] model to the dispersion auto-analysis. This is the Miloushev and Palmer 2005 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_auto-analysis.* Added the '[[MP05' ]] model to the relax user manual. This is the Miloushev and Palmer 2005 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_manual. The '[[MP05' ]] model was already partly in the manual, however it was listed as unimplemented. All of the tables and the dispersion chapter text has been updated for the model.* Modified the R1rho_analysis.py sample script to use the '[[MP05' ]] model. This is the Miloushev and Palmer 2005 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_sample_scripts.

* The '[[MP05' ]] and '[[NS R1rho 2-site' ]] are now nested in the dispersion auto-analysis. As the '[[MP05' ]] model is valid across all times scales and does not require skewed populations, its optimised parameters can be used as the starting point of optimisation of the '[[NS R1rho 2-site' ]] numeric model. This results in huge speed ups of the numeric model as previously a grid search was being performed.

* Added the '[[TAP03' ]] model to the dispersion variables. This is the Trott, Abergel and Palmer 2003 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Adding_the_model_to_the_list.* Added the '[[TAP03' ]] model to the relax_disp.select_model user function frontend. This is the Trott, Abergel and Palmer 2003 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_disp.select_model_user_function_front_end.* Added support for the '[[TAP03' ]] model to the relax_disp.select_model user function back end. This is the Trott, Abergel and Palmer 2003 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_disp.select_model_user_function_back_end.* Created the '[[TAP03' ]] model target function. This is the Trott, Abergel and Palmer 2003 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_target_function.* Added the '[[TAP03' ]] R_2eff calculating function to the relax library. This is the Trott, Abergel and Palmer 2003 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_library.* Debugging of the '[[TAP03' ]] dispersion model - optimisation is now setup correctly. This is the Trott, Abergel and Palmer 2003 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax.html#Debugging.* Debugging of the '[[TAP03' ]] dispersion model. Removed a Unicode character from the lib.dispersion.tap03 module docstring to allow it to be used in Python 2. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax.html#Debugging.

* Many fixes for the lib.dispersion.tap03 module to match the original equations. The '[[TAP03' ]] model solution is now similar to those of '[[TP02' ]] and '[[MP05']].* Updated the Relax_disp.test_tp02_data_to_tap03 system test numbers to match the optimised values. These were so close to the [[MP05 ]] model values that the test was passing anyway.* Added the '[[TAP03' ]] model to the GUI model list. This is the Trott, Abergel and Palmer 2003 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_GUI.* Added the '[[TAP03' ]] model to the dispersion auto-analysis. This is the Trott, Abergel and Palmer 2003 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_auto-analysis.* Added the '[[TAP03' ]] model to the relax user manual. This is the Trott, Abergel and Palmer 2003 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_manual. The '[[TAP03' ]] model was already partly in the manual, however it was listed as unimplemented. All of the tables and the dispersion chapter text has been updated for the model.* Added the '[[TAP03' ]] and '[[MP05' ]] models to the abbreviations in the user manual.

* Implemented the '[[MMQ 2-site' ]] CPMG model equations from the Korzhnev et al., 2005 reference. The paper reference is "Dmitry M. Korzhnev, Philipp Neudecker, Anthony Mittermaier, Vladislav Yu. Orekhov, and Lewis E. Kay (2005). Multiple-site exchange in proteins studied with a suite of six NMR relaxation dispersion experiments: An application to the folding of a Fyn SH3 domain mutant. J. Am. Chem. Soc., 127, 15602-15611. (doi: http://dx.doi.org/10.1021/ja054550e)". The original code from Mathilde Lescanne and Dominique Marion has only slightly been modified for this change as the MQ data treatment in the Korzhnev et al., 2004 reference is the same as in the 2005 reference, but using a different notation. This has been renamed to r2eff_mmq_2site_mq(). The new r2eff_mmq_2site_sq_dq_zq() function has been added to the lib.dispersion.mmq_2site module to allows the SQ, DQ, and ZQ R_2eff data to be calculated. This function follows the notation of the 2005 paper. The populate_matrix() function has been modified to only accept one combined chemical shift difference value. It can now also accept different values for R_2A⁰ and R_2B⁰, though the mmq_2site module defaults to R_2A⁰=R_2B⁰.

* Simplified the '[[MMQ 2-site' ]] dispersion model target function. The r2eff_mmq_2site_sq_dq_zq() and r2eff_mmq_2site_mq() functions from lib.dispersion.mmq_2site are now aliased by the experiment_type_setup() target function method. Both functions now have matching arguments.

* Created the Relax_disp.test_korzhnev_2005_15N_sq_data system test. This is used to check the optimisation of the 15N SQ CPMG data using the '[[MMQ 2-site' ]] model.

* Created 5 more system tests for checking the optimisation of single sets of Korzhnev et al., 2005 data. These are Relax_disp.test_korzhnev_2005_15n_dq_data, Relax_disp.test_korzhnev_2005_15n_mq_data, Relax_disp.test_korzhnev_2005_15n_zq_data, Relax_disp.test_korzhnev_2005_1h_mq_data, and Relax_disp.test_korzhnev_2005_1h_sq_data. These should individually test out all parts of the '[[MMQ 2-site' ]] dispersion model.

* The '[[MMQ 2-site' ]] dispersion model can now be optimised if no heteronuclear R_2eff data is loaded.

* Updated the synthetic '[[TP02' ]] model data for the recent changes.

* Updated all of the relax results for the [[IT99 ]] model fix.* Added the new relax [[IT99 ]] model results to the software_comparison file. This is for the truncated CPMG data from Flemming Hansen.* Fix for the [[LM63 ]] dispersion model equation in the manual.* The [[CR72 ]] dispersion model descriptions now emphasise the fact that it is not accurate on all time scales. This is for the dispersion chapter of the user manual.* Modified the relax_disp.select_model user function [[CR72 ]] model descriptions. Instead of saying all time scales, the '[[CR72']], '[[CR72 full']], and '[[MQ CR72' ]] model descriptions instead now say most time scales.

* Another bug fix for the [[IT99 ]] model. This was pointed out by Nikolai Skrynnikov that the omega_1eff definition is incorrect and instead it should be omega_1eff = 4 * sqrt(3) * nu_CPMG.* Updated the Relax_disp.test_hansen_cpmg_data_to_it99 system test for the [[IT99 ]] model fixes.* Updated the relax results for the truncated CPMG data from Flemming Hansen. This is needed as the [[IT99 ]] model has been fixed and the new relax_disp.write_disp_curves user function introduced.

* Created the Relax_disp.test_korzhnev_2005_all_data system test for checking the '[[MMQ 2-site' ]] model. This checks against all six data types, 1H SQ, 15N SQ, DQ, ZQ, 1H MQ, and 15N MQ. This is currently set to the values found by cpmg_fit. As this is the true solution, relax should find similar parameter values.

* Created a script to compare the cpmg_fit and relax solutions for the '[[MMQ 2-site' ]] dispersion model.

* Bug fix for the '[[MMQ 2-site' ]] dispersion model target function. The relaxation time was being taken as that of the first experiment for all experiments. This is a relic from the code being copied from a single experiment type model.* Converted the '[[MQ CR72' ]] dispersion model to handle MMQ data. This model can now handle proton-heteronuclear SQ, ZQ, DQ, and MQ CPMG-type data. Some debugging might still be required.* Fix for the '[[MQ CR72' ]] model for MQ-type data. The check to prevent acos of a number less than 1 has been changed to switch the sign rather than to set the back calculated R_2eff to 1e99.* Another bug fix for the '[[MQ CR72' ]] dispersion model. The nu_CPMG value rather than the relaxation time was being used to calculate the R_2eff values as the division by 'n' was missing.

* Fixes for the '[[MQ CR72' ]] dispersion model target function.* Removed a latent bug in the '[[MMQ 2-site' ]] dispersion model. This was not being seen but might have caused problems in the future.* Fix for the '[[MQ CR72' ]] dispersion model target function. The correct R₂⁰ values are now extracted from the parameter vector.* Improvements for the '[[CR72' ]] and '[[MQ CR72' ]] dispersion model R_2eff calculating functions. The numpy.arccosh() function can handle all input values when complex, therefore the checks for the real part being above 1 are not necessary.

* Changed the sign of the delta_omega frequency for the ZQ data in the '[[CR72' ]] and '[[MQ CR72' ]] models.* Last fix for the '[[MQ CR72' ]] dispersion model. The wrong value was being subtracted from the first eigenvalue - the value of log(Q)/relax_T should not be divided by the number of CPMG blocks.* Simplified the first '[[MQ CR72' ]] dispersion model formula in the manual.* Created a relax script to compare the '[[MQ CR72' ]] dispersion model results to cpmg_fit. The cpmg_fit solution is used as the input parameters for relax, and then a calc user function call is used to back calculate the R_2eff values. These values are then plotted to show the perfect match.* Bug fixes for the '[[MMQ 2-site' ]] dispersion model. The matrix power factor must be found with the Python math.floor() function and not int() as the later will sometimes round up.

* Fixes for the relaxation dispersion system tests for the changed behaviour of the '[[CR72' ]] model. The optimisation is slightly different as values are now always passed into the numpy.arccosh() function.

* Updated the Relax_disp.test_sprangers_data_to_mq_cr72 system test to pass. The '[[MQ CR72' ]] model is now much more accurate due to a number of recent bug fixes.

* The relax_disp.plot_disp_curves user function now produces interpolated dispersion curves. For this the new 'num_points' and 'extend' arguments have been added to the user function to give the user better control of this plotting. The interpolated curve is disabled from the numeric CPMG models as these do not support interpolation, and the '[[R2eff' ]] model as interpolation is not needed. To support this, the specific_analyses.relax_disp.optimisation.back_calc_r2eff() function has been extended to support the CPMG frequencies or spin-lock field strengths been supplied instead of retrieved. This allows a set of custom dispersion points to be used in the back calculation. The dispersion target function setup was modified to prevent the recalculation of tau_CPMG values when asked, as interpolation is not compatible with this.

* Merged the '[[MQ CR72' ]] dispersion model into the MMQ data type sections in the tables of the manual.

* Updates for the '[[MMQ 2-site' ]] model equations in the manual.