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Internal links to the dispersion models.
* Python 3 fixes for the info module. The new processor_name() function was not compatible with Python 3 as the text read from STDOUT needs to be 'decoded'.
* The variables in the relax_fit.h file are now all static.
* Added the new exp_mc_sim_num argument to the relaxation dispersion auto-analysis. This is in preparation for fixing [https://gna.org/bugs/?21869 bug #21869]. This argument allows for a different number of Monte Carlo simulations for the '[[R2eff' ]] model when exponential curves are fit. It will mainly be useful in the test suite to improve the accuracy of the R2eff errors, while still running a low number of simulations for the other models to allow optimisation to be quick.* Modifications to the Relax_disp.test_m61_exp_data_to_m61 system test. This is to fix [https://gna.org/bugs/?21869 bug #21869], the failure of this system test. The number of Monte Carlo simulation for the '[[R2eff' ]] model has been increased from 3 to 25 using the new exp_mc_sim_num argument to the dispersion auto-analysis. To keep the test fast, only a single spin is optimised.
* Redesign and major clean up of the specific_analyses.jw_mapping package. The code has been broken up into separate modules.
* Fix for the default value table documentation in the specific_analyses.jw_mapping package. This was broken in the last commit.
* The R2eff dispersion parameter now also defaults to 10 rad.s^-1.
* Expanded the dispersion specific API set_param_values() method for the 'r2eff' and 'i0' parameters. This now sets these parameter values correctly if the value sent into the method is not composed of dictionaries.
* Large speed up of the relaxation dispersion system tests by about 20%. This was achieved by turning the grid search off in the following system tests: Some of the optimisation values are slightly different, or completely different for the one example of the [[CR72 ]] model fitted to no exchange, and these have been updated in the tests.
* Changed the bounds for the R20 parameters in the default grid search. The range of 1 to 40 rad.s^-1 was previous used. This has been narrowed to 5 to 20.
* Added function to find minimum R2eff value to set as R20 value before grid search. [https://gna.org/support/?3151 Support request #3151, user function to set the R<sub>2</sub><sup>0</sup> parameters in the default grid search using the minimum R<sub>2eff</sub> value].
* Added MODEL_B14 to specific_analyses.relax_disp.variables. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales].
* Further added info for MODEL_B14 to specific_analyses.relax_disp.variables. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales].
* Added [[B14 ]] description to the [http://www.nmr-relax.com/manual/relax_disp_select_model.html relax_disp.select_model user function] front end. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales].* Added model [[B14 ]] to be found as target function. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales].
* Added empty b14.py to relax library lib/dispersion/b14.py. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales].
* Extended docstring in b14.py file. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales].
* Implemented start system test for model [[B14]]. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. System test is Relax_disp.test_baldwin_synthetic.* Added Baldwin model [[B14 ]] test data. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales].
* Removed MODEL_B14 to be tested in normal setup. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This is to allow the system test to pass.
* Removed the standard transparent "on" setting in grace images script file. This was rather an annoyance than helpful.
* Docstring update for the test suite runner class - the verification tests are now listed.
* Added the software verification tests to the relax GUI. The verification tests can now be selected via the "Tools->Test suite->Verification tests" menu entry. Running the full test suite via the menus also now included the verification tests.
* Reordered the [[B14 ]] model according to release year. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. 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 B14 model is explained in: http://wiki.nmr-relax.com/B14.* Redid ordering of Model model [[B14 ]] according to release year. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. 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 B14 model is explained in: http://wiki.nmr-relax.com/B14.* Reordered the model [[B14 ]] according to release year. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. 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 B14 model is explained in: http://wiki.nmr-relax.com/B14.* Reordered model [[B14 ]] in target functions. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. 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 B14 model is explained in: http://wiki.nmr-relax.com/B14.* Python API documentation corrections for the model [[B14]]. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. 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 B14 model is explained in: http://wiki.nmr-relax.com/B14.* Replaced copyright notice for the Baldwin.py script. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. 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 B14 model is explained in: http://wiki.nmr-relax.com/B14.* Changed the compression back 9, when creating grace PNG files. It doesn't change the quality, just the time to create the file and the size of the file. PNG is lossless, so compression levels 1 to 9 are all pixel-perfect. The B14 model is explained in: http://wiki.nmr-relax.com/B14.
* Added a check for the existence of data pipes to the return_api() specific analysis function.
* Added a README file to the sample_scripts directory to help users understand what these scripts are for. It also explains how these scripts should be used.
* Implemented synthetic CPMG system test. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. 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 B14 model is explained in: http://wiki.nmr-relax.com/B14.* Small changes to synthetic script data generator. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. 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 B14 model is explained in: http://wiki.nmr-relax.com/B14.
* Made synthetic CPMG script accept R2eff noise values as input.
* Added array with zero R2eff error to system test Relax_disp.test_cpmg_synthetic.
* Added a row to the dispersion software comparison table for TROSY-type data. This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/5414/focus=5501.
* Added a row to the dispersion software comparison table for the support of scalar coupling effects. This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/5414/focus=5501.
* Added model [[B14 ]] to the list of MODEL_LIST_NUMERIC_CPMG. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax. Model [[B14]], uses the number of ncyc/CPMG blocks in its analytical equation. To pass this information correct and calculate the ncyc power, it should be in this list. The B14 model is explained in: http://wiki.nmr-relax.com/B14.* Letting the error be 0.1 in the system test for [[B14]]. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax. This is just cosmetics, to make the dispersion graph look more beautiful. The B14 model is explained in: http://wiki.nmr-relax.com/B14.* Implemented model [[B14 ]] in the relax library. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_library. The code is raw implemented, with no optimisation. This is merely to test, that the spin parameters that created R2eff data, can be found again after grid search and minimisation. The B14 model is explained in: http://wiki.nmr-relax.com/B14.* Correctly implemented the target function for model [[B14]]. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. 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. The B14 model is explained in: http://wiki.nmr-relax.com/B14.* Implemented system test "relax -s Relax_disp.test_baldwin_synthetic -d" for model [[B14]]. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging. This proves that the model is correctly implemented, and return same data which the Baldwin script created. The B14 model is explained in: http://wiki.nmr-relax.com/B14.
* Renamed the [http://www.nmr-relax.com/manual/relax_disp_cpmg_frq.html relax_disp.cpmg_frq user function] to [http://www.nmr-relax.com/manual/relax_disp_cpmg_setup.html relax_disp.cpmg_setup] and added some new options. This follows from the thread http://thread.gmane.org/gmane.science.nmr.relax.devel/5511/focus=5520. The ncyc_even option has been added so the user can specify if the pulse sequence requires an even number of CPMG blocks. This is for use in the interpolated dispersion curves, but could have other uses in the future.
* Removed model [[B14 ]] to the list of MODEL_LIST_NUMERIC_CPMG. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax. This was not essential anyway.
* Changed the default value of pA, the population for state A, to 0.95. When doing a grid search in the auto-analysis, one can set "None". This will then use default values specified for parameters, instead of a grid search. pA is best to start at 0.95, than 0.5.
* Extended system test Relax_disp.test_baldwin_synthetic to also include a N15 synthetic dataset. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Modified system_tests/scripts/relax_disp/cpmg_synthetic.py and the corresponding system tests. Relax_disp.test_cpmg_synthetic_cr72. Relax_disp.test_cpmg_synthetic_cr72_full_noise_cluster. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Attempt to implement function map_bounds in API for relax_disp. [https://gna.org/bugs/?22012 Bug #22012: dx.map not implemented for pipe type relax_disp].
* Expanded the '[[CR72 full' ]] dispersion model description in the manual to explain its origin. This was discussed at http://thread.gmane.org/gmane.science.nmr.relax.devel/5410. The equations used the Davis et al., 1994 simplified form, and this is now explained.
* Changed float powers of 2.0 to integer powers of 2, to speed up the calculations. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This change did not do a large change in speed, but is more proper. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Changed all instances of "r2e" with "r20b", to be consistent with relax nomenclature. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Changed all instances of R2g with r20a. This is to be consistent with the relax nomenclature. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Implemented g3 and g4 as square root functions instead of atan2. atan2 is always returning values between -pi and pi. https://docs.python.org/2/library/math.html. Next step is to convert g1>-g1, which will truly follow the [[CR72 ]] Nomenclature. For this, the atan2 function is a blocker. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Had to lower the precision of system test Relax_disp.test_baldwin_synthetic. This was after changing g3, and g4 from atan2 functions, to square root functions. The model is still very precise though. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Altered the sign of g1, to follow [[CR72 ]] Nomenclature. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Had to lower the precision of system test Relax_disp.test_baldwin_synthetic after sign change of g1. The model is still precise, finding the parameters which generated the data. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Made g2 use the [[CR72 ]] parameter convention. No change detected, since the change will be erased by going to order**2. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.* Made sign change of deltaR2, to use parameter convention of [[CR72]]. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.* Implemented the alpha minus shorting from [[CR72]]. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Pretty the code, making space between all multiplications "*". [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Pretty up the code, making space between "=". [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Fixed the average position Euler angles for the rotor2 CaM frame order test data optimisation script. The angles needed to be reversed.
* Removed an duplicated chi2 printout in the rotor2 CaM frame order test data optimisation script.
* Speedup - made [[B14 ]] use the pre-calculated inverse time, instead of calculating the inverse time inside the function. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Speedup - moved the repetitive calculations of pB, k_BA and k_AB out of the library function. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Speedup - moved the calculation of deltaR2 and alpha_m out of library function. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Speedup - repetitive calculations of sqrt_zeta2_Psi2 = sqrt(zeta2 + Psi2). [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Speedup - converted expressions of complex(x, y) to (x + y*1j). [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Split the func_B14 into full, with a calc function. This is to prepare for the splitting up of [[B14]], into a full: R2a!=R2b, and "normal" which is r2a=r2b. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.* Documentation fix for [[CR72 ]] calc function.* Renamed system test Relax_disp.test_baldwin_synthetic to Relax_disp.test_baldwin_synthetic_full. And changed model from "[[B14 full|B14" ]] to "[[B14 full"]]. This is to help find where modifications now have to be changed. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Added B14_FULL to the lists of the specific_analyses.relax_disp.variables module. The model name is stored in a special variable which will be used throughout relax. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. 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 B14_FULL to the [http://www.nmr-relax.com/manual/relax_disp_select_model.html relax_disp.select_model user function] front end. Added the model, its description, the equations for the analytic models, and all references to the [http://www.nmr-relax.com/manual/relax_disp_select_model.html relax_disp.select_model user function] front end. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. 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 B14_FULL to the target function. The system test Relax_disp.test_baldwin_synthetic_full is now back and running. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. 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.
* Implemented system test Relax_disp.test_baldwin_synthetic for the model [[B14]], whereby the simplification R20A = R20B is assumed. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Added target function for the Baldwin (2014) 2-site exact solution model for all time scales, whereby the simplification R20A = R20B is assumed. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. 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.
* Finished system test Relax_disp.test_baldwin_synthetic. This proves that model [[B14 ]] whereby the simplification R20A = R20B is assumed is successfully implemented. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.* Added the synthetic data for [[B14 ]] model whereby the simplification R20A = R20B is assumed. This is used in system test Relax_disp.test_baldwin_synthetic. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Added B14 and B14_FULL to the relax GUI. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. 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 latex bibliography reference for the model [[B14]]. This is the reference for Baldwin (2014) B14 model - 2-site exact solution model for all time scales. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. 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.* Added model [[B14 ]] description in the manual. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. 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.
* Updated the references in the b14.py library file, to point to the wiki, and the future API and html documentation. The link to API and html documentation is to be updated for the future compilation of these. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. 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.
* Reinserted the library function of b14.py the calculation of: deltaR2 = r20a - r20b; alpha_m = deltaR2 + k_AB - k_BA; zeta = 2 * dw * alpha_m; and Psi = alpha_m**2 + 4 * k_BA * k_AB - dw**2. And put the g_fact = 1/sqrt(2), inside the library function. It made no sense to put these calculations outside the library, since there would be no skipping of a loop. It actually makes much better sense to keep these calculation in the library function, to preserve the possibility to import this module in other software. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Changed manual, to the recipe at Appendix 1. This was changed after the wish of the author. Discussed in: http://thread.gmane.org/gmane.science.nmr.relax.devel/5632. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. 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.
* Changed that taucpmg = 1 / 4*nucpmg and not taucpmg = 1 / nucpmg. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. 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.
* Added model [[B14 ]] to the list of dispersion models. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. 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.* Relax manual fix for model [[TSMFK01]]. Added that the model is slow exchange.* Fix for equation alignment for model [[B14]]. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. 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.
* Elimination of minus in library function b14.py. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Replaced f0 with F0, to follow paper and relax manual. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Replaced "ex0c" with "v1s" to follow manual and paper. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Replaced f2 with F2, to follow manual and paper. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Sqrt fix in manual for model [[B14]]. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Fix for ordering in calculation, to make it look prettier. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Replaced "v2pPdN" with v5, to follow paper and manual. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Speedup by removing integer to float conversion part.
* Better latex2html support for the relax manual, specifically the dispersion software comparison table. The \yes and \no commands are now better processed as HTML, and the rotating package 'rotate' environment is replaced by nothing. This will improve the dispersion software comparison table at http://www.nmr-relax.com/manual/Comparison_dispersion_analysis_software.html.
* Fix for catastrophic parameter index error for model [[B14]]. The model [[B14 ]] would get the same parameter index as "[[B14 full"]], and would hence optimise wrong parameters. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.* Fix for model [[B14 ]] making ugly graphs. The power of ncyc has to be an integer. [https://gna.org/bugs/?22018 Bug #22018: Model B14 creates ugly graphs ! Sig saw all over the place].* Fix for model [[B14 full ]] making ugly graphs. The power of ncyc has to be an integer. [https://gna.org/bugs/?22018 Bug #22018: Model B14 creates ugly graphs ! Sig saw all over the place].
* Fixes for the HTML version of the relax manual. The renewal of the \theequation command in the model-free and relaxation dispersion chapters was causing all equation numbers in latex2html to be broken. By placing these in a latexonly environment, the problem is avoided in the HTML version at www.nmr-relax.com/manual/.
* Changed script for synthetic CPMG data. This is to test the fitting of [[CR72 ]] and [[B14]], when creating R2eff data with numerical model: MODEL_NS_CPMG_2SITE_EXPANDED. This script is ideal for testing cases. One can readily define experiments settings: sfrq_X, time_T2_X, ncycs_X for simulating one or more spectrometer experiments. Spins can readily be set up, to have different dynamics, like: r2, r2a, r2b, kex, pA and dw. The script can test clustering, and can convert to Sherekhan and make a hyper-dimensinal dx map to test Chi2 hypersurface on parameter settings. It is also ideal for strees-testing relax, to see if its minimisation algorithm performs well. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Small improvement for generic CPMG data script file. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Added functionality of the visualising the spin dynamics point which generated the data. This is to the script, which can visualize the synthetic CPMG data. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Added list_of_lists to uf_objects. [https://gna.org/task/?7791 Task #7791, the dx.map should accept a list of list with values for points].
* Made multiple writing of point files. [https://gna.org/task/?7791 Task #7791, the dx.map should accept a list of list with values for points].
* Added [[B14 ]] to the dispersion software comparison table in the manual (docs/latex/dispersion_software.tex). [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. 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.* Added [[B14 ]] to the dispersion auto-analysis. The B14 models will not create output files until this is done. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. 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
* Completely removed the list_of_lists argument. [https://gna.org/task/?7791 Task #7791, the dx.map should accept a list of list with values for points].
* Modified the description of making x,y,z points in the chi2 space for the [http://www.nmr-relax.com/manual/dx_map.html user function dx.map]. [https://gna.org/task/?7791 Task #7791, the dx.map should accept a list of list with values for points].
* Made solutions for math domain error. Prevented to take log of negative values, and division by zero. This though slows the implementation down. System test Relax_disp.test_baldwin_synthetic_full went from 6.x seconds to 8-9.x seconds. [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Changed an 'align' environment to 'equation' as there was only one equation.
* Removed invisible equations from the [[B14 ]] dispersion model section of the relax manual. The trailing "\\" were causing equation numbers to be produced on empty lines after the block of equations.* The f00 equation in the [[B14 ]] dispersion model section of the manual is a single equation. The 'subequations' and 'align' environments are therefore superfluous.
* Modified dx.map to accept more than one point. [https://gna.org/task/?7791 Task #7791, the dx.map should accept a list of list with values for points].
* Added system test for the production of dx map. Relax_disp.test_cpmg_synthetic_dx_map_points. [https://gna.org/task/?7791 Task #7791, the dx.map should accept a list of list with values for points].
* Added proper punctuation to the [[B14 ]] dispersion model equations in the manual. Equations should be readable as English sentences and they follow standard punctuation rules. All of the equations in the [[B14 ]] model section of the dispersion chapter have been updated to follow this.* Fixes for quotation marks in the [[B14 ]] dispersion model section of the manual. LaTeX requires `' for single quotes rather than ''.* Standardised the [[CR72 ]] R2eff factor in the [[B14 ]] dispersion model section of the manual. This is now defined in the preamble of the LaTeX manuscript.* Converted all complex numbers 'i' in the [[B14 ]] dispersion model section of the manual to \imath.* Removed some unnecessary {} brackets from the user manual. This is for the [[B14 ]] model (http://wiki.nmr-relax.com/B14) section of the dispersion chapter.* The ncyc variable is now defined in the LaTeX preamble. This is for the [[B14 ]] model (http://wiki.nmr-relax.com/B14) section of the dispersion chapter.* Fixes for some of the maths in the [[B14 ]] model section of the dispersion chapter.* Fix for the arccosh operator in the [[B14 ]] section of the manual. This is for the [[B14 ]] model (http://wiki.nmr-relax.com/B14) section of the dispersion chapter.* Switched to using the LaTeX math symbol for real numbers \Re. This is for the [[B14 ]] model (http://wiki.nmr-relax.com/B14) section of the dispersion chapter.
* The Ncyc definition in the manual now uses a capital N.
* The \arccosh LaTeX maths operator is now defined in the preamble of the manual. This is used by the [[B14 ]] model (http://wiki.nmr-relax.com/B14) section of the dispersion chapter.* Improved brackets for the [[B14 ]] model (http://wiki.nmr-relax.com/B14) section of the dispersion chapter. The \left( and \right) command are used to produce brackets that scale to the size of the maths within these brackets. One set of unneeded brackets were also removed.* Grammar fixes for the [[B14 ]] model (http://wiki.nmr-relax.com/B14) section of the dispersion chapter.* Added some text explaining why the [[B14 ]] equations do not look like those of the paper. This is for the [[B14 ]] model (http://wiki.nmr-relax.com/B14) section of the dispersion chapter.* Small edits to the text of the [[B14 ]] dispersion model section of the manual.* Replaced 'get' and 'got' with alternatives, as this verb is not to be used in formal English. This is for the [[B14 ]] model (http://wiki.nmr-relax.com/B14) section of the dispersion chapter of the manual.* Clean ups of the Carver and Richards descriptions. This is for the [[B14 ]] model (http://wiki.nmr-relax.com/B14) section of the dispersion chapter of the manual.* More basic editing of the text of the [[B14 ]] dispersion model section of the manual.
* The T_relax symbol is now defined in the preamble of the manual. This is to standardise its usage in the dispersion chapter.
* Major fix for the R2eff equations for the [[B14 ]] dispersion model in the manual. Here tau_CPMG, the time for one CPMG block, was mixed up with T_relax, the total time of all CPMG blocks.* Switched some 'v' symbols to '\nu' in the [[B14 ]] dispersion model section of the manual.* Standardised the spacing in the equations for the [[B14 ]] dispersion model in the manual.* Clean ups for the end of the [[B14 ]] dispersion model section of the manual. Here a number of 'v' were changed to \nu and the standard \kAB, \pA, and \pB are now used.* Some more tau_CPMG verses T_relax fixes for the [[B14 ]] dispersion model equations in the manual.* Added some symmetry to the T equation in the [[B14 ]] dispersion model section of the manual.
* Latex2html fixes for the HTML version of the relax manual. This is for the documentation at http://www.nmr-relax.com/manual/index.html. Latex2html has problems determining if the contents of environments should added to the sub or superscript. For example $1^\textrm{st}$ is not recognised and must be changed to $1^{\textrm{st}}$ for latex2html to function correctly. Therefore these problems have been fixed throughout the manual. The number of errors printed out by latex2html is now significantly less.
* Shifted the model-free model equations for the HTML manual to the subequations environment. This is for the relax manual at http://www.nmr-relax.com/manual/index.html This is to preserve the equation numbering so that the HTML and PDF equation numbers match as closely as possible.
* Python 3 fix for the Relax_disp.test_kteilum_mhsmith_eschulz_lcchristensen_gsolomentsev_moliveberg_makke_sod1wt_t25_to_cr72 system test. The xrange builtin function does not exist in Python 3.
* Python 3 fix for the Relax_disp.setup_sod1wt_t25 system test. The xrange builtin function does not exist in Python 3.
* Updated the Relax_disp.test_hansen_cpmg_data_missing_auto_analysis system test for the recent changes. This is for fixing [https://gna.org/bugs/?21960 bug #21960]. The chi-square values are different due to the fix for [https://gna.org/bugs/?21954 bug #21954, the peak intensity error analysis bug], and the [[CR72 ]] model (http://wiki.nmr-relax.com/CR72) results are different due to the fix for [https://gna.org/bugs/?21953 bug #21953, the change of the kex values used in the grid search].* Fix for the [http://www.nmr-relax.com/manual/relax_disp_select_model.html relax_disp.select_model user function] for when the C modules are not compiled. This was checking for the presence of the compiled C modules whenever the '[[R2eff' ]] model was specified. However this behaviour is incorrect. It should only check for the C modules if exponential curves are to be fit.
* Fix for bug. The variances used to calculated std, should only be taken from those which are defined in the subset. Regarding [https://gna.org/bugs/?21954 bug #21954, order of spectrum.error_analysis is important].
* Fix for system test Relax_disp.test_hansen_cpmgfit_input. [https://gna.org/bugs/?21989 Bug #21989, relax_disp.cpmgfit_input does not work for model CR72]. The looping was performed over the file lines instead of the defined fixed lines. The output files is truncated, and does not contain the wished data.
* Fix for [https://gna.org/bugs/?22004 bug #22004, the conformation_analysis_rdc+pcs.py N-state model sample script not working]. The problem was that the return_api() function call needed to be after the creation of the data pipe.
* Fix for the local_min_search.py N-state model sample script. The return_api() function call was preformed too early. Instead of placing it after the data pipe creation, the specific analysis type is now directly specified.
* Fix for type in the eta scale of [[CR72 ]] model. The calculation in relax was correct, but the scale of eta has been wrong in the documentation. This was discussed in: http://thread.gmane.org/gmane.science.nmr.relax.devel/5506. The B14 model is explained in: http://wiki.nmr-relax.com/B14.
* Bug fix for taking the median if there is more than 0 values in the list. [https://gna.org/bugs/?22010 Bug #22010: relax_disp.parameter_copy return a list of pA, if copying only for one spin].
* Fix for the dispersion model_statistics() specific API method. The spin ID argument should override the model_info argument. The method now correctly implements this.
* Added another sentence telling the user that multiple field relaxation data is essential. This is for the model-free dauvergne_protocol auto-analysis section of the relax manual and relates to [https://gna.org/bugs/?21799 bug #21799].
* Another sentence about multiple field relaxation data added to the manual. This is for the model-free dauvergne_protocol GUI section of the relax manual and relates to [https://gna.org/bugs/?21799 bug #21799].
* Documentation fix for [[IT99]]. Changed kex to tex. Still needs to be changed at homepage: http://www.nmr-relax.com/analyses/relaxation_dispersion.html#IT99. [https://gna.org/bugs/?22019 Bug #22019: the IT99 model is listed with parameter kex instead of tex].* Documentation fix for [[IT99]]. Changed kex to tex in user function. [https://gna.org/bugs/?22019 Bug #22019: the IT99 model is listed with parameter kex instead of tex].
* Small extra explanation in auto analysis. [https://gna.org/bugs/?21799 Bug #21799: Insufficient recommendations/warning message for the execution of dauvergne protocol with 1 field is incomplete].
* Big bug fix for the relax installation path determination. This is to fix [http://gna.org/bugs/?22037 bug #22037, the failure to load graphics in the GUI due to the relax installation path not being set up correctly]. The problem is that the status module was looking for the compat.py file to determine where the base directory is, but this file has been moved into the lib/ package. Now the dep_check.py file is being searched for.
