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Changes
Improved link formatting.
* Updated the results of relax's analysis of the truncated CPMG data from Flemming Hansen.
* Updates for the model variable docstrings.
* Added the 'M61 skew' model to the specific_analyses.relax_disp.variables module. This is the Meiboom 1961 model for skewed populations (p<sub>A</sub> ≫ p<sub>B</sub>). This commit follows step 1 of the relaxation dispersion model addition tutorial ([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<sub>A</sub> ≫ p<sub>B</sub>). This commit follows step 2 of the relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].
* Fixes for the spacing after some equations in the relax_disp.select_model docstring.
* Simplifications and comment fixes in the lib.dispersion.m61.r2eff_m61() function.
* Renamed the lib.dispersion.m61.r2eff_M61() function to r1rho_M61().
* Added the M61 skew model equations to the relax library. This is the Meiboom 1961 on-resonance 2-site model for skewed populations (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)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<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)relaxation dispersion model addition tutorial].
* Added support for the skewed condition (p<sub>A</sub> ≫ p<sub>B</sub>) to the specific_analyses.relax_disp.parameters module. This is currently done by constraining p<sub>A</sub> to be greater than 0.85.
* 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<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)relaxation dispersion model addition tutorial].
* Big speeds ups of the lib.dispersion modules. Many replicated calculations have been shifted outside of the dispersion point loop, as these only need to be calculated once per function call. Some if statements have consequently been simplified.
* Renamed the lib.dispersion.equations module to lib.dispersion.two_point.
* Renamed the r1rho_on_res dispersion test suite data directory to r1rho_on_res_m61.
* Created test data for the 'M61 skew' R<sub>1ρ</sub> model. This is the Meiboom 1961 on-resonance 2-site model for skewed populations (p<sub>A</sub> ≫ p<sub>B</sub>). This commit follows step 7 of the relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].* Created the Relax_disp.test_r1rho_on_res_fixed_time_m61b system test. This is for the Meiboom 1961 on-resonance 2-site model for skewed populations (p<sub>A</sub> ≫ p<sub>B</sub>). This commit follows step 7 of the relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].
* Small simplification of the lib.dispersion.m61b module.
* Fix for the specific_analyses.relax_disp.disp_data.return_value_from_frq_index() function. This cdp.spectrometer_frq_list list structure rather than the cdp.spectrometer_frq dictionary should be used.
* Small changes to the r1rho_on_res_m61b dispersion test data. One R<sub>2</sub><sup>0</sup> rate has been increased.
* Completed the lib.dispersion.m61.r1rho_M61() function. Now the R<sub>1</sub> relaxation rate and rotating frame tilt angle are correctly handled. This is not used in the target functions as support for the R<sub>1</sub> and offset is not yet implemented.
* Added the 'DPL94' model to the specific_analyses.relax_disp.variables module. This is the David, Perlman and London 1994 R<sub>1ρ</sub> 2-site fast exchange model. This commit follows step 1 of the relaxation dispersion model addition tutorial ([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<sub>1ρ</sub> 2-site fast exchange model. This commit follows step 2 of the relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].
* Updates to the Relax_disp.test_r1rho_on_res_fixed_time_m61b system test.
* Added the DPL94 model equations to the relax library. This is the David, Perlman and London 1994 R<sub>1ρ</sub> 2-site fast exchange model. This commit follows step 3 of the relaxation dispersion model addition tutorial ([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<sub>1ρ</sub> 2-site fast exchange model. This commit follows step 4 of the relaxation dispersion model addition tutorial ([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<sub>1ρ</sub> 2-site fast exchange model. This commit follows step 6 of the relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].* Created the Relax_disp.test_r1rho_on_res_fixed_time_dpl94 system test. This is the David, Perlman and London 1994 R<sub>1ρ</sub> 2-site fast exchange model. This commit follows step 7 of the relaxation dispersion model addition tutorial ([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<sub>A</sub> ≫ p<sub>B</sub>. This commit follows step 1 of the relaxation dispersion model addition tutorial ([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<sub>A</sub> ≫ p<sub>B</sub>. This commit follows step 2 of the relaxation dispersion model addition tutorial ([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 R<sub>1ρ</sub>-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<sub>A</sub> ≫ p<sub>B</sub>. This commit follows step 2 of the relaxation dispersion model addition tutorial ([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<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)relaxation dispersion model addition tutorial].* Added the it99 module to the lib.dispersion package __all__ list. 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)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<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)relaxation dispersion model addition tutorial].* 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)relaxation dispersion model addition tutorial].* 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)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<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)relaxation dispersion model addition tutorial].* 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)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<sub>A</sub> ≫ p<sub>B</sub>.
* Fix for the relax_disp.cpmgfit_input user function for when no directory is given. This was causing tracebacks.
* 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.
* Fixes for the dispersion specific code. The Grace graph code of lib.software.grace no longer accepts the axis min and max arguments.
* Created the Relax_disp.test_bug_20889_multi_col_peak_list system test to catch bug #20889. The report is [https://gna.org/bugs/?20889bug #20889].
* Fixes for the Relax_disp.test_bug_20889_multi_col_peak_list GUI test.
* Fixes for the checks of the Relax_disp.test_bug_20889_multi_col_peak_list GUI test. Intensity errors will not have been calculated yet, and the structure is called baseplane_rmsd anyway.
* Fix for the Relax_disp.test_bug_20889_multi_col_peak_list GUI test. The peak intensity wizard _ok() method is now called to terminate the wizard. Otherwise this causes the subsequent GUI test which tries to access the peak intensity wizard to fail.
* Created the Relax_disp.test_hansen_cpmg_data_IT99 system test. This is for testing the Ishima and Torchia 1999 2-site model for all timescales with p<sub>A</sub> ≫ p<sub>B</sub>. This commit follows step 7 of the relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].
* Initialised the relaxation dispersion chapter in the relax manual.
* Added 600x600 pixel version of the relaxation dispersion analysis graphic. This is for use in the relax manual.
* Expanded the modelling of dispersion data section of the relax user manual.
* Expansion of the modelling of dispersion data section of the relax user manual.
* The relaxation dispersion auto-analysis now outputs text and Grace files for all parameters. This is in response to bug #20917 ([https://gna.org/bugs/?20917) bug #20917] submitted by Troels Linnet (https://gna.org/users/tlinnet).
* The Monte Carlo simulations now generate parameter errors for the relaxation dispersion analysis. The simulation index was being ignored, hence the input data was never the randomised data and all errors were zero.
* Removed many decimal points from the MHz value in the Grace plots from relax_disp.plot_disp_curves.
* Fix for the dispersion auto-analysis - p<sub>A</sub> and p<sub>B</sub> parameters are no longer output for the IT99 model. These are not parameters of this model.
* Updated the relax results for Flemming Hansen's truncated CPMG data for all the recent changes.
* Fix for bug #20916, [ (https://gna.org/bugs/?20916) bug #2091] - Suggestion for Python script for PNG/EPS/SVG conversion of grace files. Troels Linnet provided this patch, and was discovered during work on a Windows 7 system. This patch will provide a grace2images.py file in each folder where a call to specific_analyses/relax_disp/disp_data.py is called. It is called in plot_disp_curves(dir=None, force=None) and call the function lib.software.grace.script_grace2images(). The conversion script can be executed in Linux and Windows, if the PATH to xmgrace has been specified. It will look in a folder for grace files of ending *.agr and by default convert to PNG. One can also convert to EPS and SVG. Probably more options could be added, as PDF. The conversion depends on xmgrace compilation, and so PNG conversion is for fast inspection of graphs in folder, and EPS for further external conversion to PDF etc. The patch, the output file, and small script to test is attached. I miss to make the file executable in relax, so the script can be executed directly in Linux.
* Mac OS X bug fix for the new analysis GUI wizard. The blank button is now using the blank_150x150.png file instead of no image, preventing nasty wxPython bugs from appearing on that system.
* Fix for bug #20917 ([https://gna.org/bugs/?20917)bug #20917]. The problem is that the Grace files for each spin system are not created by the relax_disp.plot_disp_curves user function as the ':' character cannot be placed in a file name in MS Windows. All of the file name from the ':' onwards is lost. The solution is to replace each of the characters '#:@' in the spin ID string with '_'.
* Another update of the relax results for Flemming Hansen's truncated CPMG data. This includes the grace2images.py script creation contributed by Troels Linnet (https://gna.org/users/tlinnet) and the change of the file name of the per-spin dispersion curves.
* The value checks in the Relax_disp.test_hansen_cpmg_data_auto_analysis system test are now less precise. This is to allow the tests to pass on certain MS Windows systems.
* Fix for the setting of the execute permissions on the grace2images.py scripts. The problem was identified in the post at http://thread.gmane.org/gmane.science.nmr.relax.devel/3953/focus=4000. This is within the relax_disp.plot_disp_curves user function after the grace2images.py script has been created. The commit matches the changes from trunk for the Modelfree4 batch script.
* Shifted from argparse to optparse in the grace2images.py scripts from relax_disp.plot_disp_curves. This is associated with bug #20916 ([https://gna.org/bugs/?20916) bug #20916] and the change suggested in the post http://thread.gmane.org/gmane.science.nmr.relax.devel/3953/focus=4000. The argparse module is only available from for Python 2.7.3 (the version with many Python 3 features backported) and Python ≥ 3.2. The module has been replaced with the similar optparse module as used by relax, and which available in all Python version supported by relax.* Updated the grace2images.py scripts created by the relax_disp.plot_disp_curves user function. This was discussed in bug #20916 ([https://gna.org/bugs/?20916) bug #20916] and the change suggested in the post http://thread.gmane.org/gmane.science.nmr.relax.devel/3953/focus=4000. Improved that both small and big letters for image types can be used on the command line.
* Converted the relaxation dispersion chapter of the user manual to the lstlisting environment. This matches the changes occurring within the trunk.
* Added an EPS version of the 128x128 cluster icon for the user manual.
* Loosened a parameter check in the Relax_disp.test_hansen_cpmg_data_IT99 system test to pass on certain Linux systems.
* Small edit of the legend of the relaxation dispersion figure showing the Ishima & Torchia 2005 being wrong.
* Added [https://gna.org/users/pasa Paul Schanda's ] code for the numerical solution to the Bloch-McConnell equations for 2-sites. This is specifically code which uses complex conjugate matrices. The code was submitted at http://thread.gmane.org/gmane.science.nmr.relax.devel/4132.
* Made the lib.dispersion.ns_2site_star module importable in the absence of Scipy.
* Polished the lib.dispersion.ns_2site_star module docstring.
* Added some code missing from the lib.dispersion.ns_2site_star module. This code was accidentally not copied from http://thread.gmane.org/gmane.science.nmr.relax.devel/4132.
* Significant speed ups of the lib.dispersion.ns_2site_star.r2eff_ns_2site_star() function. Replicated calculations have been minimised.
* Added the '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 relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].
* Added the lib.dispersion.ns_2site_star module name to the package __all__ list.
* Updated the lib.dispersion.ns_2site_star module with additional information from [https://gna.org/users/pasa Paul Schanda]. The details come from http://thread.gmane.org/gmane.science.nmr.relax.devel/4132/focus=4135. The exchange-free R<sub>2</sub> value parameter names have been changed to match the convention of the other lib.dispersion modules.* Added the '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 relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].
* Fix for the non-ASCII character '\xe2' in the lib.dispersion.ns_2site_star module.
* Created the '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 relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].* Added support for the R<sub>2B</sub><sup>0</sup> parameter as required by the '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 relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].* Added support for the '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 relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].
* Better support for the R<sub>2A</sub><sup>0</sup> and R<sub>2B</sub><sup>0</sup> relaxation rate parameters in the relaxation dispersion analysis. This includes a number of fixes to allow these two parameters to be handled correctly.
* Added parameter conversions to go from p<sub>A</sub> and k<sub>ex</sub> to k<sub>ge</sub> and k<sub>eg</sub>. This is for the '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.
* Added the missing mpower() function as lib.linear_algebra.matrix_power.square_matrix_power(). This is needed by the lib.dispersion.ns_2site_star module. The function comes from the '[https://gna.org/support/download.php?file_id=18263 fitting_main_kex.py]' file attached to comment 3 of task #7712 ([https://gna.org/task/?7712#comment3, https://gna.org/support/download.php?file_id=18263)comment 3 of task #7712]. The mpower() function was copied and modified to suite relax's coding conventions.
* Added a module docstring to lib.linear_algebra.matrix_power.
* Created the lib.dispersion.ns_matrices module. This module contains a collection of functions for generating the relaxation matrices for the numerical solutions to the Bloch-McConnell equations for relaxation dispersion. The code comes from the '[https://gna.org/support/download.php?file_id=18263 fitting_main_kex.py]' file attached to https://gna.org/task/?7712#comment3(https://gna.org/support/download.php?file_id=18263).
* Docstring fix for the lib.dispersion.ns_matrices.rcpmg_2d() function.
* Added the functions for creating the X-axis pi-pulse rotation matrices in lib.dispersion.ns_matrices. The code comes from the '[https://gna.org/support/download.php?file_id=18263 fitting_main_kex.py]' file attached to https://gna.org/task/?7712#comment3(https://gna.org/support/download.php?file_id=18263).* Huge amounts of documentation added to the lib.dispersion.ns_2site_star module. This comes from Paul Schanda's ([https://gna.org/users/pasa) Paul Schanda's] post at http://thread.gmane.org/gmane.science.nmr.relax.devel/4132/focus=4152
* Spacing fixes for the lib.dispersion.ns_2site_star module as determined by the 2to3 program. This is the Python 2 to 3 conversion program.
* Docstring fix for the lib.dispersion.ns_2site_star.r2eff_ns_2site_star() function.
* Changed 'numerical integration' to 'numerical solutions' in the dispersion chapter of the manual.
* 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 2-site star' numerical model. The model and parameter tables have been updated as well.
* Added the '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<sub>2A</sub><sup>0</sup> = R<sub>2B</sub><sup>0</sup> is assumed. This commit follows step 1 of the relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].
* Rewrote the relax_disp.select_model user function documentation. All of the detailed model information has been removed as it is now in the relax user manual. The model lists have been modified to match the analytic-numeric sectioning of the manual.
* Added the '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<sub>2A</sub><sup>0</sup> = R<sub>2B</sub><sup>0</sup> is assumed. This commit follows step 2 of the relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].
* Docstring fix for the lib.dispersion.ns_2site_star.r2eff_ns_2site_star() function.
* Created the '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<sub>2A</sub><sup>0</sup> = R<sub>2B</sub><sup>0</sup> is assumed. The code in common with the 'NS 2-site star' model has been shifted into the new calc_ns_2site_star_chi2() method. This commit follows step 4 of the relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].* Added support for the '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<sub>2A</sub><sup>0</sup> = R<sub>2B</sub><sup>0</sup> is assumed. This commit follows step 6 of the relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].* Added the '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<sub>2A</sub><sup>0</sup> = R<sub>2B</sub><sup>0</sup> is assumed. This commit follows step 2 of the relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].
* Fix for the Monte Carlo simulations for the numeric dispersion models. The back-calculation method was not correctly initialising the target function class.
* Added the 'CR72 red' model to the specific_analyses.relax_disp.variables module. This is the Carver and Richards 1972 analytic model with the simplification R<sub>2A</sub><sup>0</sup> = R<sub>2B</sub><sup>0</sup>. The current 'CR72' makes the same assumption, but that model will be expanded to support R<sub>2A</sub><sup>0</sup> and R<sub>2B</sub><sup>0</sup> later. This commit follows step 1 of the relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].* Added the '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<sub>2A</sub><sup>0</sup> = R<sub>2B</sub><sup>0</sup>. The current 'CR72' makes the same assumption, but that model will be expanded to support R<sub>2A</sub><sup>0</sup> and R<sub>2B</sub><sup>0</sup> later. This commit follows step 2 of the relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].* Created the 'CR72 red' model target function. This is the Carver and Richards 1972 analytic model with the simplification R<sub>2A</sub><sup>0</sup> = R<sub>2B</sub><sup>0</sup>. The current 'CR72' makes the same assumption, but that model will be expanded to support R<sub>2A</sub><sup>0</sup> and R<sub>2B</sub><sup>0</sup> later. The code in common with the CR72 model has been shifted into the new calc_CR72_chi2() method. This commit follows step 4 of the relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].* Added support for the '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<sub>2A</sub><sup>0</sup> = R<sub>2B</sub><sup>0</sup>. The current 'CR72' makes the same assumption, but that model will be expanded to support R<sub>2A</sub><sup>0</sup> and R<sub>2B</sub><sup>0</sup> later. This commit follows step 6 of the relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].* Added the 'CR72 red' model to the relax user manual. This is the Carver and Richards 1972 analytic model with the simplification R<sub>2A</sub><sup>0</sup> = R<sub>2B</sub><sup>0</sup>. The current 'CR72' makes the same assumption, but that model will be expanded to support R<sub>2A</sub><sup>0</sup> and R<sub>2B</sub><sup>0</sup> later. This commit follows step 2 of the relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].
* LaTeX improvements for the 'NS 2-site star red model' section of the dispersion chapter of the manual.
* Expanded the CR72 model to handle both the R<sub>2A</sub><sup>0</sup> and R<sub>2B</sub><sup>0</sup> parameters. The 'CR72 red' model now functions as the old CR72 model where R<sub>2A</sub><sup>0</sup> = R<sub>2B</sub><sup>0</sup> = R<sub>2</sub><sup>0</sup>. 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<sub>2A</sub><sup>0</sup> = R<sub>2B</sub><sup>0</sup>.
* Improvements for the write_results() method of the dispersion auto-analysis. The parameter value and Grace files are now correctly created for all the recent models.
* 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 red' model.
* Added the '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 relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].* Added the '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 relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].* Added the 'NS 2-site' R<sub>2eff</sub> 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 relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].
* Updates and fixes for the lib.dispersion.ns_2site module. The function has been renamed, and the R<sub>1</sub> arguments default to 0.0. The flip angle for the from the pulse.
* Created the '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 relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].
* Converted the 'NS 2-site' model to 'NS 2-site 3D' to be more specific. This might change again in the future.
* Added support for the '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 relaxation dispersion model addition tutorial ([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 2-site 3D' model.
* Improvements to the nesting() method of the relaxation dispersion auto-analysis. The use of the parameters of the simpler model in a nested pair now only works if the simpler model is in the model list.
* Converted the pi-pulse propagator matrices to numpy array format. This is to enable the use of the much faster numpy.dot() function for performing the dot products.
* Speed ups for the '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.
* Modified the df, fA, and fB parameters to match the relax omega conventions of δω, wA, and wB. This follows from [https://gna.org/users/pasa Paul Schanda's ] confirmation at http://thread.gmane.org/gmane.science.nmr.relax.devel/4132/focus=4159.
* Speed up for the lib.dispersion.ns_matrices.rcpmg_3d() function. The p<sub>A</sub> and p<sub>B</sub> parameters are now sent into the function rather than being recreated by the function.
* More changes to the numerical solution dispersion code to match relax's conventions. This includes the changes of df->δω, fA->wA, fB->wB, and Mgx->Mx.
* Added the 'NS 2-site 3D red' model to the specific_analyses.relax_disp.variables module. This is the 'NS 2-site 3D' model with R<sub>2A</sub><sup>0</sup> = R<sub>2B</sub><sup>0</sup> = R<sub>2</sub><sup>0</sup>. This commit follows step 1 of the relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].* Added the 'NS 2-site 3D red' model to the relax_disp.select_model user function frontend. This is the 'NS 2-site 3D' model with R<sub>2A</sub><sup>0</sup> = R<sub>2B</sub><sup>0</sup> = R<sub>2</sub><sup>0</sup>. This commit follows step 2 of the relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].* Created the 'NS 2-site 3D red' model target function. This is the 'NS 2-site 3D' model with R<sub>2A</sub><sup>0</sup> = R<sub>2B</sub><sup>0</sup> = R<sub>2</sub><sup>0</sup>. This commit follows step 4 of the relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].* Added support for the 'NS 2-site 3D red' model to the relax_disp.select_model user function back end. This is the 'NS 2-site 3D' model with R<sub>2A</sub><sup>0</sup> = R<sub>2B</sub><sup>0</sup> = R<sub>2</sub><sup>0</sup>. This commit follows step 6 of the relaxation dispersion model addition tutorial ([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 2-site 3D' and 'NS 2-site 3D red' models.
* Updated the 'NS 2-site 3D' and '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 support for nesting to the relaxation dispersion auto-analysis for the 'NS 2-site 3D*' models.
* Added the '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 relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].* Added the '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 relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].* Added the 'NS 2-site expanded' R<sub>2eff</sub> 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 relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].
* Fix for the lib.dispersion.ns_2site_expanded.r2eff_ns_2site_expanded() function. The pg variable should have been p<sub>A</sub> and it needs to be sent into the function.
* Created the '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 relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].* Added support for the '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 relaxation dispersion model addition tutorial ([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 2-site expanded' model. There is only one R<sub>2</sub><sup>0</sup> parameter as R<sub>2A</sub><sup>0</sup> = R<sub>2B</sub><sup>0</sup> in this model.
* Added the '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 relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].
* Large renaming of the relaxation dispersion models. This includes both the analytic and numerical models. All of the models with separate R<sub>2A</sub><sup>0</sup> and R<sub>2B</sub><sup>0</sup> parameters now have ' full' added to the end of the model name. And all of the corresponding reduced models whereby R<sub>2A</sub><sup>0</sup> = R<sub>2B</sub><sup>0</sup> = R<sub>2</sub><sup>0</sup> have had the trailing ' red' removed. All descriptions and variable names have been updated to match.
* Updated the dispersion auto-analysis write_results() method for the recent model changes.
* Sectioning improvements for the relaxation dispersion chapter of the relax user manual.
* Added DOI numbers to a number of bibliography entries for quick links in the relax user manual.
* 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 relaxation dispersion model addition tutorial ([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 relaxation dispersion model addition tutorial ([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 relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].* Added the 'LM63 3-site' R<sub>2eff</sub> 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 relaxation dispersion model addition tutorial ([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 relaxation dispersion model addition tutorial ([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 relaxation dispersion model addition tutorial ([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 relaxation dispersion model addition tutorial ([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 relaxation dispersion model addition tutorial ([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.
* The relaxation dispersion auto-analysis can now resume if it has been interrupted.
* Updated the numeric model results for the software_comparison file.
* 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).
* Added Dominique Marion to the copyright notices of all the lib/dispersion/ns_*.py files. This is in response to [https://gna.org/users/pasa Paul Schanda's ] message at http://thread.gmane.org/gmane.science.nmr.relax.devel/4225/focus=4226.
* Small fix for the relax_disp.cluster documentation.
* Added the new pre_run_dir argument to the relaxation dispersion auto-analysis. This is to enable clustered optimisation. This specifies a directory containing a completed analysis. The parameters from this previous run will be used as the starting point for optimisation of the clustered analysis.
* Added links to all of the copyright licensing agreements for the lib.dispersion.ns_2site_expanded module.
* Added Nikolai Skrynnikov to the copyright notice of the lib.dispersion.ns_2site_expanded module.
* Added the 'TP02' model to the specific_analyses.relax_disp.variables module. This is the Trott and Palmer 2002 R<sub>1ρ</sub> analytic model for 2-site exchange. This commit follows step 1 of the relaxation dispersion model addition tutorial ([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<sub>1ρ</sub> analytic model for 2-site exchange. This commit follows step 2 of the relaxation dispersion model addition tutorial ([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<sub>1ρ</sub> analytic model for 2-site exchange. This commit follows step 2 of the relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].* Added the 'TP02' R<sub>1ρ</sub>' calculating function to the relax library. This is the Trott and Palmer 2002 R<sub>1ρ</sub> analytic model for 2-site exchange. This commit follows step 3 of the relaxation dispersion model addition tutorial ([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 2-site expanded' model to the CPMG dispersion sample script.
* Converted the lib.dispersion.tp02 module from Matlab code to Python. The code has also been made fail-safe and repetitive calculations have been shifted outside of the loop to speed things up.
* 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<sub>1ρ</sub> analytic model for 2-site exchange. This commit follows step 4 of the relaxation dispersion model addition tutorial ([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<sub>1ρ</sub> analytic model for 2-site exchange. This commit follows step 6 of the relaxation dispersion model addition tutorial ([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.
* Turned off clustering in the Relax_disp.test_r1rho_off_res_fixed_time_tp02 system test. This speeds the test up by more than half.
* 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.
* Attempt at fixing bug #21080 ([https://gna.org/bugs/?21080)bug #21080]. This was reported by Troels Linnet. The problem is a standard GUI problem. The text from a wxPython GUI is a Unicode string. But relax requires standard strings. Therefore the gui.string_conv.gui_to_str() function needs to be used on the return value of the GUI element GetValue() method, but this call was forgotten.
* 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 r1rho_on_res_m61.py system test script. The spins are now different residues. This fixes two system tests.
* Renamed all of the current numeric dispersion models in relax to be specific to CPMG-type data. This is in preparation for adding R<sub>1ρ</sub> numeric models. It was proposed at http://thread.gmane.org/gmane.science.nmr.relax.devel/4461.
* 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<sub>1ρ</sub> data. This commit follows step 1 of the relaxation dispersion model addition tutorial ([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<sub>1ρ</sub> data. This commit follows step 2 of the relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].* Added the 'NS R1rho 2-site' R<sub>1ρ</sub> calculating function to the relax library. This is the numerical model for the 2-site Bloch-McConnell equations for R<sub>1ρ</sub> 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 relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].
* Fix for the function name in the lib.dispersion.ns_r1rho_2site module and removed misplaced copyrights.
* Created the 'NS R1rho 2-site' model target function. This is the numerical model for the 2-site Bloch-McConnell equations for R<sub>1ρ</sub> 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 relaxation dispersion model addition tutorial ([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<sub>1ρ</sub> 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 relaxation dispersion model addition tutorial ([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<sub>1ρ</sub> 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 relaxation dispersion model addition tutorial ([http://thread.gmane.org/gmane.science.nmr.relax.devel/3907)relaxation dispersion model addition tutorial].
* Rearrangement of the model sections in the dispersion chapter of the user manual. These are now better separated into different categories.
* 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.
* Renamed many of the Relax_disp system tests to bring some order to the naming.
* Alphabetical ordering of all of the Relax_disp system tests.
* Created a system test to catch bug #21081 ([https://gna.org/bugs/?21081)bug #21081]. This uses a truncated version of Troel Linnet's save state attached to the bug report (the data pipes not used in the model selection have been manually deleted as well as all by the first 3 spins in the remaining 2 data pipes).* Fix for bug #21081 ([https://gna.org/bugs/?21081) bug #21081] - the failure of a dispersion cluster analysis. The problem was that the specific_analyses.relax_disp.disp_data.loop_cluster() generator method was not taking the spin.select flag into account. Now all deselected spins are excluded from the spin clusters and the free spins.
* Better support for off-resonance R<sub>1ρ</sub> data in the dispersion GUI. A new row of buttons has been added to the dispersion GUI, just above the Peak list GUI element. The first button is for the spin.isotope user function and replaces the old GUI element. Two new buttons for loading R<sub>1</sub> data and chemical shifts have also been added, as required for off-resonance R<sub>1ρ</sub> data.
* Changed the chemical shift icon to that of the chemical shift in ppm units - the delta symbol.
* A bit of help for some of the R<sub>1ρ</sub> dispersion model system tests. These now fail after a fundamental fix. The problem is only due to the very coarse grid search size - a finer grid search allows the solution to be correctly found. However as this is far too slow, instead the k<sub>ex</sub> parameter is set to be close to the solution to skip a grid search dimension.
* Some basic fixes for the Relax_disp.test_hansen_catia_input system test. The relax_disp.catia_input user function is not complete, but this allows the Relax_disp system tests to pass.
* The dispersion multi-processor optimisation code now prints out its own simulation messages. This is to fix bug #21190 ([https://gna.org/bugs/?21190)bug #21190]. The memo object now is feed in the spin IDs of the cluster and stores this as the cluster_name variable. This is used by the results object run() method, which is run on the master at the end, to print out a message along the lines of "Simulation X, cluster yyy". Therefore the message is only printed out once the calculation of that slave command is complete and returned to the master.
* Replaced all usage of scipy.linalg.expm() with lib.linear_algebra.matrix_exponential.matrix_exponential(). This is for the functions of the lib.dispersion package used for the relaxation dispersion numeric solution models. The change eliminates a bug in the scipy function which uses the Pade approximation which fails horribly for the complex part of the matrix. The real part looks good, but the complex part looks to have nasty truncation artefacts which is propagated and amplified through the Bloch-McConnell equations.
* Modified the Relax_disp.test_sprangers_cpmg_data_auto_analysis system test so the models are programatically changed.