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* 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 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.
* 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 [https://{{gna.org/task/?link|7712#comment3 |comment=3|text=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/?url|7712#comment3|comment=3}}.
* 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/?url|7712#comment3|comment=3}}.
* Huge amounts of documentation added to the lib.dispersion.ns_2site_star module. This comes from {{relax developer link|username=pasa|text=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.
* 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|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, {{relax developer link|username=pasa|text=Paul Schanda}}, and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://{{gna.org/task/?url|7712#comment2 |comment=2}} 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 [http://www.nmr-relax.com/manual/relax_disp_select_model.html 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, {{relax developer link|username=pasa|text=Paul Schanda}}, and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://{{gna.org/task/?url|7712#comment2 |comment=2}} 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<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, {{relax developer link|username=pasa|text=Paul Schanda}}, and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://{{gna.org/task/?url|7712#comment2 |comment=2}} 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].
* 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 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, {{relax developer link|username=pasa|text=Paul Schanda}}, and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://{{gna.org/task/?url|7712#comment2 |comment=2}} 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 [http://www.nmr-relax.com/manual/relax_disp_select_model.html 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, {{relax developer link|username=pasa|text=Paul Schanda}}, and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://{{gna.org/task/?url|7712#comment2 |comment=2}} 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.
* 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.
* 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 [http://www.nmr-relax.com/manual/relax_disp_select_model.html 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<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, {{relax developer link|username=pasa|text=Paul Schanda}}, and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://{{gna.org/task/?url|7712#comment2 |comment=2}} 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].
* 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 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, {{relax developer link|username=pasa|text=Paul Schanda}}, and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://{{gna.org/task/?url|7712#comment2 |comment=2}} 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 [http://www.nmr-relax.com/manual/relax_disp_select_model.html 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, {{relax developer link|username=pasa|text=Paul Schanda}}, and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://{{gna.org/task/?url|7712#comment2 |comment=2}} 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 [http://www.nmr-relax.com/manual/relax_disp_select_model.html relax_disp.select_model user function] for the [[NS CPMG 2-site expanded|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 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, {{relax developer link|username=pasa|text=Paul Schanda}}, and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://{{gna.org/task/?url|7712#comment2 |comment=2}} 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].
* 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.
* 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 [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].
* Added the [[NS R1rho 2-site]] model to the [http://www.nmr-relax.com/manual/relax_disp_select_model.html 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 [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/?url|7712#comment5|comment=5}}). 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].
* 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/?url|7712#comment5|comment=5}}). 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 [http://www.nmr-relax.com/manual/relax_disp_select_model.html 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/?url|7712#comment5|comment=5}}). 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<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/?url|7712#comment5|comment=5}}). This commit follows step 2 of the [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.
* Enabled the parallelisation of Monte Carlo simulations for the relaxation dispersion analysis.
* Created a set of scripts for testing out the multi-processor abilities of the dispersion analysis.
* Added Remco Sprangers' truncated ClpP data to test_suite/shared_data/dispersion/Spranger_ClpP. This is the data attached to https://{{gna.org/task/?url|7712#comment6|comment=6}}, and it will be used for testing the implementation of the [[NS MMQ 2-site|MQ NS 2-site]] model, when added to relax.
* Concatenated the peak intensity files.
* 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.
* Added the Tollinger et al., 2001 reference for the [[NS CPMG 2-site expanded]] model. This reference was communicated in a private email.
* Improvements for the LaTeX maths commands used in the dispersion chapter of the user manual.
* Added Skrynnikov and Tollinger to the copyright notice in lib/dispersion/ns_cpmg_2site_star.py. I can now see that the code derives from the funNumcpmg.m of the sim_all.tar file (https://gna.org/support/download.php?file_id=18404) attached to https://{{gna.org/task/?url|7712#comment5|comment=5}}. This sim_all.tar file is the original code of Nikolai and Martin.
* 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.
* Used the \imath LaTeX symbol for complex numbers in the dispersion chapter of the manual.
* Created a 'TODO' section in the dispersion chapter of the relax user manual. This lists all of the features and models currently missing from the dispersion analysis in relax.
* Added the original Maple script to the lib.dispersionns_cpmg_2site_expanded module docstring for reference. This was sent by Nikolai in a private communication.
* More expansion of the lib.dispersionns_cpmg_2site_expanded module docstring for reference. The link https://{{gna.org/task/?url|7712#comment8 |comment=8}} to the p3.analytical script in the Gna! tasks has been added and the contents of the sim_all.tar file funNikolai.m has been copied into the docstring as well.
* Epydoc docstring fixes to allow the API documentation to be properly compiled.
* Python 3 fix for the lib.dispersion.mq_ns_cpmg_2site module. The numpy.linalg.matrix_power requires an integer power, but Python 3 was creating a floating point number for the 'fact' variable.
