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* Modified system test Relax_disp.test_r1rho_kjaergaard to use input guess values of phi_ex in units of ppm^2 instead of rad^2/s^2.
* Small change to system test Relax_disp.test_r1rho_kjaergaard. The outcome of kex from system test is in the area of 4-5000. The expected value is 13000. A deeer analysis of the input is needed, to judge what is the correct value.
* Created the Structure.test_bug_21814_pdb_no_80_space_padding system test. This is for catching bug #21814 ([https://gna.org/bugs/?21814)bug #21814, the PDB reading failure when the PDB records are not padded to 80 spaces]. The PDB file used for the test is the same file as attached to the bug report.
* The verbosity flag is now used in the centre of mass calculations. The pipe_control.structure.mass.pipe_centre_of_mass() function now passes the verbosity argument into the lib.structure.mass.centre_of_mass() function.
* Created the new vector_angle() library function. This is located in the lib.geometry.vectors module. The function will calculate the angle between two vectors with sign or direction using the atan2() function.
* Improvements for the pipe_control.mol_res_spin.generate_spin_id_unique() function. The unique spin ID now takes into account if the molecule is named or not (for single molecules). This allows the function to be used when dealing with the structural data rather than the molecule, residue, and spin data structure.
* Removed the full stop from the printout of the test names in the test suite. This allows for quicker copying and pasting of the test name when running with the --time option and then selecting a single test to run.
* Modified the Noe.test_noe_analysis system test to catch bug #21863 ([https://gna.org/bugs/?21863). This is bug #21863, the failure to create the ref and sat Grace 2D plots in the NOE analysis].* Improved the user feedback when executing a user function in the GUI. The busy cursor is now turned on at the start of the user function wizard page method _apply() and turned off again at the end. This would avoid user confusion, thinking that the program has frozen (as was the case in bug #21862, [https://gna.org/bugs/?21862bug #21862]).* Changed the Noe.test_noe_analysis system test to handle the peak intensities correctly. This relates to bug #21863 ([https://gna.org/bugs/?21863)bug #21863, the grace.write user function not being able to write ref/sat plots as described in sample script noe.py]. Instead of trying to produce the 'ref.agr' and 'sat.agr' files for the non-existent 'ref' and 'sat' parameters, instead the 'intensities.agr' file is being produced for the peak intensity parameter. The reference and saturated intensities will appear as two graph sets within that plot.* Changed the Noe analysis sample script to properly handle the peak intensity Grace plots. This relates to bug #21863 ([https://gna.org/bugs/?21863)bug #21863, the grace.write user function not being able to write ref/sat plots as described in sample script noe.py]. Instead of trying to produce the 'ref.agr' and 'sat.agr' files for the non-existent 'ref' and 'sat' parameters, instead the 'intensities.agr' file is being produced for the peak intensity parameter. The reference and saturated intensities will appear as two graph sets within that plot. These changes match those of the test suite.
* Fix for the line numbering for the NOE analysis sample script in the user manual. The line numbering for the code snippets did not match that of the full sample script shown at the start of that section of the NOE chapter.
* Added a simple shell script to quickly grep the entire source tree while excluding .svn directories. This will only work on POSIX systems (Linux and Macs).
* Fix for the Noe.test_bug_21562_noe_replicate_fail system test. The 'ref' and 'sat' parameters do not exist. Therefore the [http://www.nmr-relax.com/manual/grace_write.html grace.write user function] calls in the system test script have been modified to output the 'intensities' parameter instead.
* Complete rearrangement of the specific analysis code for the steady-state NOE. This brings the code into line with the recent specific analysis code rearrangements, specifically in the specific_analyses.relax_disp package.
* Changed the Noe auto-analysis to properly handle the peak intensity Grace plots. This relates to bug #21863 ([https://gna.org/bugs/?21863)bug #21863, the grace.write user function not being able to write ref/sat plots as described in sample script noe.py]. Instead of trying to produce the 'ref.agr' and 'sat.agr' files for the non-existent 'ref' and 'sat' parameters, instead the 'intensities.agr' file is being produced for the peak intensity parameter. The reference and saturated intensities will appear as two graph sets within that plot.
* Redesign and standardisation of the peak intensity data structure throughout all analyses in relax. The various structures 'intensities', 'intensity_err', 'intensity_sim', 'sim_intensity', and 'intensity_bc' have all been renamed. The new structures are called 'peak_intensity', 'peak_intensity_err', 'peak_intensity_sim' and 'peak_intensity_bc'. This allows the structure to be processed as a standard parameter in the specific analysis API. One very visible consequence is that plots of peak intensities, as well as value files, will now have peak intensity errors. For backwards compatibility, the relax data store method _back_compat_hook() has been modified to catch all previous peak intensity object variants and to standardise and rename these to the new object names. As the parameter is now called 'peak_intensity' rather than 'intensities', all calls to the grace.write and value.write for this parameter have been changed in the auto-analyses, the sample scripts, the test suite and the manual.
* Fix for the Noe.test_noe_analysis system test. The grace plots of the peak intensities now have error bars.
* 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 bug #21869 ([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 bug #21869 ([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.
* Added system test to analyse data. System test for CPMG dataset, (http://dx.doi.org/10.1073/pnas.0907387106) Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C. Christensen, Gleb Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009 SOD1-WT at 25 C.
* The debugging command line option no longer turns on RelaxWarning tracebacks. These tracebacks can be separately turned on with the --traceback command line option.
* Made name for system test shorter and moved data to shorter folder name. Regarding bug #21953, ([https://gna.org/bugs/?21953) - bug #21953, weird performance of grid search].* Modified system test for cleaner implementation of tests. Regarding bug #21953, ([https://gna.org/bugs/?21953) - bug #21953, weird performance of grid search].* Lowered range for grid search by factor 10 for kex to now between 1-10000. Regarding bug #21953, ([https://gna.org/bugs/?21953) - bug #21953, weird performance of grid search].* Changes to system test Relax_disp.test_hansen_cpmg_data_auto_analysis. Regarding bug #21953, ([https://gna.org/bugs/?21953) - bug #21953, weird performance of grid search]. The grid search needed to be increased by +1 and lowering of some results by one digit.* Lowering of precision in Relax_disp.test_hansen_cpmg_data_auto_analysis_numeric. Regarding bug #21953, ([https://gna.org/bugs/?21953) - bug #21953, weird performance of grid search].* Changes to system test Relax_disp.test_hansen_cpmg_data_auto_analysis_r2eff. Regarding bug #21953, ([https://gna.org/bugs/?21953) - bug #21953, weird performance of grid search]. The grid search needed to be increased by +1 and lowering of some results by one digit.* Changes to system test Relax_disp.test_hansen_cpmg_data_missing_auto_analysis. Regarding bug #21953, ([https://gna.org/bugs/?21953) - bug #21953, weird performance of grid search]. The grid search needed to be increased by +1 and changes of some results.* Modified system test Relax_disp.test_sod1wt_t25_to_cr72. Regarding bug #21953, ([https://gna.org/bugs/?21953) - bug #21953, weird performance of grid search].* Modified dw and kex in system test Relax_disp.test_tp02_data_to_tap03. Regarding bug #21953, ([https://gna.org/bugs/?21953) - bug #21953, weird performance of grid search].* Split system test Relax_disp.sod1wt_t25_to_cr72 into part as setup and test part. Regarding bug #21953, ([https://gna.org/bugs/?21953) - bug #21953, weird performance of grid search].* Started implementation of error analysis bug. Regarding bug #21954, ([https://gna.org/bugs/?21954) - bug #21954, Order of spectrum.error_analysis is important].
* Small edit of the relax command line option descriptions.
* Undid the modification of dw and kex in system test Relax_disp.test_tp02_data_to_tap03. Regarding bug #21953, ([https://gna.org/bugs/?21953) - bug #21953, weird performance of grid search]. The number of iterations needed to be increased from 2000 to 2500 to allow the values to be found.* Further extended system test Relax_disp.test_sod1wt_t25_bug_21954_order_error_analysis. Regarding bug #21954, ([https://gna.org/bugs/?21954) - bug #21954, order of spectrum.error_analysis is important].* Extended --gui-tests Relax_disp.test_hansen_trunc_data. Regarding bug #21954, ([https://gna.org/bugs/?21954) - bug #21954, order of spectrum.error_analysis is important]. To catch errors in this dataset.
* This time the blacklisted relaxation dispersion system tests have been correctly reduced. Only one blacklisted test did not require the C modules to be compiled.
* Shifted all of the dispersion model descriptions and parameter lists to the variables module. The descriptions and parameter lists which were part of the [http://www.nmr-relax.com/manual/relax_disp_select_model.html relax_disp.select_model user function] backend have been shifted into the specific_analyses.relax_disp.variables module as MODEL_DESC_* and MODEL_PARAMS_* variables. The descriptions have also all been standardised. The MODEL_DESC and MODEL_PARAMS dictionaries have also been created to hold all of the descriptions and parameters in one place.
* 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. Feature request: #3151, ([https://gna.org/support/?3151) - Support request #3151, user function to set the R20 R<sub>2</sub><sup>0</sup> parameters in the default grid search using the minimum R2eff R<sub>2eff</sub> value].* Added system test for setting R20 from minimum R2eff before grid search. Feature request: #3151, ([https://gna.org/support/?3151) - Support request #3151, user function to set the R20 R<sub>2</sub><sup>0</sup> parameters in the default grid search using the minimum R2eff R<sub>2eff</sub> value]. System test: -s Relax_disp.test_sod1wt_t25_set_grid_r20_from_min_r2eff.* Extended api value.set to use index in value setting. Feature request: #3151, ([https://gna.org/support/?3151) - Support request #3151, user function to set the R20 R<sub>2</sub><sup>0</sup> parameters in the default grid search using the minimum R2eff R<sub>2eff</sub> value]. The index used is expected to match the spectrometer frequency.* Added [http://www.nmr-relax.com/manual/relax_disp_set_grid_r20_from_min_r2eff.html user function relax_disp.set_grid_r20_from_min_r2eff]. Feature request: #3151, ([https://gna.org/support/?3151) - Support request #3151, user function to set the R20 R<sub>2</sub><sup>0</sup> parameters in the default grid search using the minimum R2eff R<sub>2eff</sub> value].* Modified system test to use user function instead. Feature request: #3151, ([https://gna.org/support/?3151) - Support request #3151, user function to set the R20 R<sub>2</sub><sup>0</sup> parameters in the default grid search using the minimum R2eff R<sub>2eff</sub> value].* Added relax_disp.set_grid_r20_from_min_r2eff functionality to the relax dispersion auto_analyses. Feature request: #3151, ([https://gna.org/support/?3151) - Support request #3151, user function to set the R20 R<sub>2</sub><sup>0</sup> parameters in the default grid search using the minimum R2eff R<sub>2eff</sub> value].* Fix for skipping grid search, when set parameter values are of dict() type. Feature request: #3151, ([https://gna.org/support/?3151) - Support request #3151, user function to set the R20 R<sub>2</sub><sup>0</sup> parameters in the default grid search using the minimum R2eff R<sub>2eff</sub> value].* Extended system test for -s Relax_disp.test_sod1wt_t25_set_grid_r20_from_min_r2eff. Feature request: #3151, ([https://gna.org/support/?3151) - Support request #3151, user function to set the R20 R<sub>2</sub><sup>0</sup> parameters in the default grid search using the minimum R2eff R<sub>2eff</sub> value]. The system test now both test the creation of the correct values, the running of grid_search, and the auto_analysis.* Added True/False button to activate relax_disp.set_grid_r20_from_min_r2eff in auto-analyses. Feature request: #3151, ([https://gna.org/support/?3151) - Support request #3151, user function to set the R20 R<sub>2</sub><sup>0</sup> parameters in the default grid search using the minimum R2eff R<sub>2eff</sub> value].* Set the verbosity=1, since the output is minimal. Feature request: #3151, ([https://gna.org/support/?3151) - Support request #3151, user function to set the R20 R<sub>2</sub><sup>0</sup> parameters in the default grid search using the minimum R2eff R<sub>2eff</sub> value].* Fix for non-existing dictionary keys causing errors. Feature request: #3151, ([https://gna.org/support/?3151) - Support request #3151, user function to set the R20 R<sub>2</sub><sup>0</sup> parameters in the default grid search using the minimum R2eff R<sub>2eff</sub> value].* Fix for setting index=None, when setting default values for parameters. Feature request: #3151, ([https://gna.org/support/?3151) - Support request #3151, user function to set the R20 R<sub>2</sub><sup>0</sup> parameters in the default grid search using the minimum R2eff R<sub>2eff</sub> value].* Parameter values pre-set to 0.0 is now skipped in grid_search. Feature request: #3151, ([https://gna.org/support/?3151) - Support request #3151, user function to set the R20 R<sub>2</sub><sup>0</sup> parameters in the default grid search using the minimum R2eff R<sub>2eff</sub> value].* Renamed system test to reflect what it is testing. Feature request: #3151, ([https://gna.org/support/?3151) - Support request #3151, user function to set the R20 R<sub>2</sub><sup>0</sup> parameters in the default grid search using the minimum R2eff R<sub>2eff</sub> value].* Better formatting of text in user function. Feature request: #3151, ([https://gna.org/support/?3151) - Support request #3151, user function to set the R20 R<sub>2</sub><sup>0</sup> parameters in the default grid search using the minimum R2eff R<sub>2eff</sub> value].* Python 3 fix. Feature request: #3151, ([https://gna.org/support/?3151) - Support request #3151, user function to set the R20 R<sub>2</sub><sup>0</sup> parameters in the default grid search using the minimum R2eff R<sub>2eff</sub> value].* Better wording of experimental feature in GUI tooltip. Feature request: #3151, ([https://gna.org/support/?3151) - Support request #3151, user function to set the R20 R<sub>2</sub><sup>0</sup> parameters in the default grid search using the minimum R2eff R<sub>2eff</sub> value].* An additional warning paragraph has been added to the user function. Feature request: #3151, ([https://gna.org/support/?3151) - Support request #3151, user function to set the R20 R<sub>2</sub><sup>0</sup> parameters in the default grid search using the minimum R2eff R<sub>2eff</sub> value].* Fix for system test Relax_disp.test_set_grid_r20_from_min_r2eff_cpmg. Feature request: #3151, ([https://gna.org/support/?3151) - Support request #3151, user function to set the R20 R<sub>2</sub><sup>0</sup> parameters in the default grid search using the minimum R2eff R<sub>2eff</sub> value]. Fixed values for testing was added.
* Improved the error reporting from the Library.test_library_independence verification test.
* Fix for setting the pre-set values in grid_search. Feature request: #3151, ([https://gna.org/support/?3151) - Support request #3151, user function to set the R20 R<sub>2</sub><sup>0</sup> parameters in the default grid search using the minimum R2eff R<sub>2eff</sub> value]. Now test that values which are of dictionary types, has more than 0 values.
* Modified system test Relax_disp.test_sod1wt_t25_to_cr72.
* Added a paragraph to the clustering section of the dispersion chapter covering parameter copying. This explains the purpose of the [http://www.nmr-relax.com/manual/relax_disp_parameter_copy.html relax_disp.parameter_copy user function].
* Created system test to catch the error -s Relax_disp.test_sod1wt_t25_to_sherekhan_input. Bug #21995: ([https://gna.org/bugs/?21995) Bug #21995: creating sherekhan input files, with data for several fields and different time_T2].* Removed the necessity that len(cdp.relax_time_list) = 1 when issuing the sherekhan input user function. Bug #21995: ([https://gna.org/bugs/?21995) Bug #21995: creating sherekhan input files, with data for several fields and different time_T2].* Made testing of files for system test -s Relax_disp.test_sod1wt_t25_to_sherekhan_input. Bug #21995: ([https://gna.org/bugs/?21995) Bug #21995: creating sherekhan input files, with data for several fields and different time_T2]. Warning, the sherekhan user function will write to current directory.* Added "dir" as input to the user function relax_disp.sherekhan_input in system test. Bug #21995: ([https://gna.org/bugs/?21995) Bug #21995: creating sherekhan input files, with data for several fields and different time_T2].* Modified the relax_disp.sherekhan_input to accept dir as input. Bug #21995: ([https://gna.org/bugs/?21995) Bug #21995: creating sherekhan input files, with data for several fields and different time_T2].* Turning off local dir writing in system test and set the correct time_T2. Bug #21995: ([https://gna.org/bugs/?21995) Bug #21995: creating sherekhan input files, with data for several fields and different time_T2].* Fix for letting ShereKhan user function write the time_T2 correct. Bug #21995: ([https://gna.org/bugs/?21995) Bug #21995: creating sherekhan input files, with data for several fields and different time_T2].* Fix for correct looping over time points, when creating ShereKhan files. Bug #21995: ([https://gna.org/bugs/?21995) Bug #21995: creating sherekhan input files, with data for several fields and different time_T2].* Added check for number of time points is 1. Bug #21995: ([https://gna.org/bugs/?21995) Bug #21995: creating sherekhan input files, with data for several fields and different time_T2].* Added model MODEL_B14 to system test Relax_disp.test_hansen_cpmg_data_auto_analysis_r2eff. Sr #3154: ([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 specific_analyses.relax_disp.variables. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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.
* Made a generic script to generate R2eff data for a CPMG model based on spin parameters, and fit the data. Still needs to implement some noise method. 1) The idea is to generate R2eff data with a numerical model with some extreme parameters. 2) Then add noise to the R2eff data. 3) Then fit with a analytical model. Evaluate the performance on the analytical model. This follows the idea of the paper: http://dx.doi.org/10.1016/j.jmr.2014.02.023 "An exact solution for R2,eff in CPMG experiments in the case of two site chemical exchange" Andrew J. Baldwin, Journal of Magnetic Resonance, 2014. The script can be extended to also include global fitting, to test this out. The script is also ideal, when trying to implement a new model, since test-data is ready at hand.
* 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. Sr #3154: ([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 B14 according to release year. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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 N15 data for system test Relax_disp.test_baldwin_synthetic. Sr #3154: ([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. Sr #3154: ([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. Bug #22012 ([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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: (https:[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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: (https[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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: (https:[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 "*". Sr #3154: ([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 "=". Sr #3154: ([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 all "-". Sr #3154: (https[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 all "+". Sr #3154: ([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.* More code clean up. Make it look pretty. Sr #3154: ([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 code, by moving comments up on line. Sr #3154: (https:[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 code. Remove trailing spaces. Sr #3154: ([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 expression with -alpha_. Sr #3154: ([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 numpy.XX functions, with just the function. Sr #3154: (https[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 "power" with ncyc and made use of numpy power. Sr #3154: ([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 code, removing multiple "(" and ")". Sr #3154: ([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 Trel with relax_time, to use relax parameter conventions. Sr #3154: (https:[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 pb and pa with relax parameter pA. Sr #3154: ([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 keg with relax parameter normal use of k_BA. Sr #3154: ([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 kge with k_AB, which is relax convention. Sr #3154: (https[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.* Removed where k_AB was subtracted with k_AB. Sr #3154: ([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 of code, replacing repetitive calculations of dw**2. Sr #3154: ([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 repetitive calculations of g3**2. Sr #3154: ([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 repetitive calculations of g4**2. Sr #3154: ([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.
* Removed the specific API method aliasing in the pipe_control.opendx module. The API object is now instead aliased as self.api.
* Docsting fixes for some model_statistics() API methods, including the base class method.
* 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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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 code. Re-ordered logic of r20 parameters, and exchange parameters in function call. Sr #3154: ([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.* Moved Carver and Richards (1972) zeta and Psi notation outside library function. Sr #3154: ([https://gna.org/support/?3154) Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales]. Not sure, if this speeds the calculation up. 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 - made variable for the repetitive calculations of zeta**2, and Psi**2. Sr #3154: ([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 - made "1" and "2" integers to float, to prevent Python conversion. Sr #3154: ([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 2.0 * tcp. Sr #3154: ([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 g_factor: g = 1/sqrt(2) outside library function to be calculated once. Sr #3154: ([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). Sr #3154: ([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). Sr #3154: ([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. Sr #3154: ([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" to "B14 full". This is to help find where modifications now have to be changed. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: (https[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. Sr #3154: ([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. Sr #3154: (https[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. Sr #3154: ([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. Sr #3154: (https[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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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.* Removed the pre-calculation of "zeta2 = zeta**2" "Psi2 = Psi**2" since it did not speed-up things. This power 2 of zeta and Psi is only done once. Sr #3154: ([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.* Used LaTeX subequations instead, and using R2eff parameter is defined in the relax.tex. Using the defined \Rtwoeff, \RtwozeroA, \RtwozeroB, \kAB, \kBA, \kex. Sr #3154: ([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.
* Fixes for all URLs in the HTML version of the relax manual. This fix will appear later at http://www.nmr-relax.com/manual/index.html once the next version of relax is released. The trick was to translate the \url{} LaTeX commands which are not recognised by latex2html into \htmladdnormallink{#1}{#1} commands using a htmlonly environment in the headers.
* The \bibitem command is no longer ignored when building the HTML version of the relax manual. This will allow the bibliography at http://www.nmr-relax.com/manual/Bibliography.html to be formatted in a reasonable way. And citations will have proper links to the entries in this file rather than the current behaviour of linking to itself, hence not going anywhere.
* Apostrophe fix in the LaTeX bibliography file. This will fix my name at http://www.nmr-relax.com/manual/Bibliography.html so that it is not displayed as d’Auvergne.
* Better latex2html support for the relax manual. The hyperlink command \href{}{} and inline bibliographic reference command \bibentry{} are now supported in the HTML version of the relax manual. These are translated into \htmladdnormallink{#2}{#1} and \citet{#1} command respectively, both of which are supported by latex2html. This will significantly improve the documentation at http://www.nmr-relax.com/manual/index.html.
* Made better notation of equation. Sr #3154: ([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 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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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 "ex0b" with "v1c" to follow paper and manual. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: (https[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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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.* Replaved "oGt2" with "v4" to follow manual and paper. Sr #3154: ([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.* Took inv_tcpmg outside parenthesis to follow manual. Sr #3154: (https[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.* Sign fix in manual. The 1/taucpmg was taken wrong outside parenthesis. Sr #3154: ([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 "t2" with "F1b" to follow paper. Sr #3154: ([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 "t1pt2" with "F1a_plus_b" for better reading. Sr #3154: ([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.* Reorder of lines to follow appendix 1 in paper. Sr #3154: ([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.* Rewrote lines to follow appendix 1 in paper. Sr #3154: (https[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 expression according to appendix 1 in manual. Sr #3154: ([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.* Replaced T_{\textrm{rel} with \taucpmg. Sr #3154: ([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.* Very small speed-up. Sr #3154: ([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. Sr #3154: ([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. Bug #22018 ([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. Bug #22018 ([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. Sr #3154: ([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. Sr #3154: ([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. Sr #3154: ([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 script for the visualising the spin dynamics point which generated the data. This is to the script, which can visualize the synthetic CPMG data. Sr #3154: ([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 the file name writing of the point file. Bug #22023: ([https://gna.org/bugs/?22023) Bug #22023: relax dx.map produce .net files which makes error].* Made system test Relax_disp.test_cpmg_synthetic_dx_map_points to start testing. Modified also sample CPMG script to allow for this. Task #7791: ([https://gna.org/task/?7791) Task #7791, the dx.map should accept a list of list with values for points].* Modified [http://www.nmr-relax.com/manual/dx_map.html user function dx.map] to accept list of lists with values. Task #7791: ([https://gna.org/task/?7791) Task #7791, the dx.map should accept a list of list with values for points].* Added is_list_val_or_list_of_list_val to lib/arg_check.py. This function is not yet done. Task #7791: ([https://gna.org/task/?7791) Task #7791, the dx.map should accept a list of list with values for points].* Added list_of_lists to user_functions/objects.py. Task #7791: ([https://gna.org/task/?7791) Task #7791, the dx.map should accept a list of list with values for points].* Added list_of_lists to uf_objects. Task #7791: ([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. Task #7791: ([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). Sr #3154: ([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. Sr #3154: ([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. Task #7791: ([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]. Task #7791: ([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. Sr #3154: ([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. Task #7791: ([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. Task #7791: ([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 ''.
* 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.
* Fixes for the equation number in the HTML version of the manual. This is for the relax manual at http://www.nmr-relax.com/manual/index.html.
* Made collecting of min, max and median value of chi2, when creating the chi2 map. Task #7792: ([https://gna.org/task/?7792) Task #7792, make the dx.map write suggest chi surface values].* Made the parsing of the min, max and median chi2 value to be used to define the chi2 hypersurfaces when writing the dx .net program. Task #7792: ([https://gna.org/task/?7792) Task #7792, make the dx.map write suggest chi surface values].
* Updated the latex2html HTML version to 4.1. This is for the relax manual at http://www.nmr-relax.com/manual/index.html.
* Removed the "remap" keyword in the dx.map function, since this is not in use. Task #7792: ([https://gna.org/task/?7792) Task #7792, make the dx.map write suggest chi surface values].* Removed the keywords for "remap" in backend function, since this was not used. Task #7792: ([https://gna.org/task/?7792) Task #7792, make the dx.map write suggest chi surface values].* Added the keyword "chi_surface" to the front-end dx.map function. To set the chi2 surface level for the innermost, inner, middle and outer isosurface. Task #7792: ([https://gna.org/task/?7792) Task #7792, make the dx.map write suggest chi surface values].* Added the chi_surface=None to the backend function. When None, it will try to find reasonable chi2 values. These will define surface levels for the innermost, inner, middle and outer isosurface. Task #7792: ([https://gna.org/task/?7792) Task #7792, make the dx.map write suggest chi surface values].* Now saves all chi2 values, to better find reasonable chi level for the innermost, inner, middle and outer isosurface. Task #7792: ([https://gna.org/task/?7792) Task #7792, make the dx.map write suggest chi surface values].* Made the standard values of chi2 surface be 10, 20, 50 and 90 percentile of all chi2 values. Task #7792: ([https://gna.org/task/?7792) Task #7792, make the dx.map write suggest chi surface values].
* Increased the precision of many of the Frame_order.test_rigid_data_to_*_model system tests. This is to fix a test which was failing due to the recent re-parameterisation of the rotor frame order model to eliminate one parameter. The precision of the numeric Sobol' sequence integration has been increased by shifting the fixed parameter values even closer to zero. As a consequence, the chi-squared value of five of these tests is now lower.
* Fix for system test Relax_dips.test_cpmg_synthetic_dx_map_points. Removing keyword "remap", since this is not in use anymore. Task #7792: ([https://gna.org/task/?7792) Task #7792, make the dx.map write suggest chi surface values].* Changed the import of percentile from lib.mathematics to lib.numpy_future. Task #7792: ([https://gna.org/task/?7792) Task #7792, make the dx.map write suggest chi surface values].* Changed the percentage which is different in percentile from numpy_future. Task #7792: ([https://gna.org/task/?7792) Task #7792, make the dx.map write suggest chi surface values].* Added lib/numpy_future.py. This module is for implementing numpy function code from higher versions of numpy. The relax dependencies listed at the download page of relax: http://www.nmr-relax.com/download.html#Source_code_release currently only requires numpy >= 1.0.4. Task #7792: ([https://gna.org/task/?7792) Task #7792, make the dx.map write suggest chi surface values].* Added "numpy_future" to the __init__.py file in lib directory. Task #7792: ([https://gna.org/task/?7792) Task #7792, make the dx.map write suggest chi surface values].* Moved numpy_future from lib to extern. Extern is special package for external software or code that is bundled with relax. Task #7792: ([https://gna.org/task/?7792) Task #7792, make the dx.map write suggest chi surface values].* Updated synthetic CPMG data script. This is to analyse complex dispersion data. Related to bug #22021: ([https://gna.org/bugs/?22021) bug #22021 model B14 shows bad fitting to data]. Bug #22024: ([https://gna.org/bugs/?22024) Bug #22024 minimisation space for CR72 is catastrophic]. The chi2 surface over dw and pA is bounded.
* Added 4 unit tests for the lib.geometry.lines.closest_point_ax() function. This relax library function was previously not being checked in the test suite.
* Modified the rotor2 CaM frame order test data optimisation script to optimise the pivot. Print statements has been added for comparing the optimised to the original pivot. The rotation axis is now also only created once, as it is now used in three places in the script, hence the two functions for converting parameters to the new parameterisation have been updated.
* Modified the rotor2 CaM frame order test data optimisation script to compare the rotor axes. The optimised rotor axis is recreated with the lib.frame_order.rotor_axis.create_rotor_axis_alpha() function, and then the original and optimised axes are compared. The [http://www.nmr-relax.com/manual/state_save.html state.save user function] has been shifted forwards in the script to avoid a later RelaxError. The log file, average position PDB file, and state file from running the script have been added to the repository or updated.
* Removed the domain rotation code from the [http://www.nmr-relax.com/manual/pymol_cone_pdb.html pymol.cone_pdb user function] backend. This should only display the cone PDB object. The domain rotation is now performed by the far more powerful [http://www.nmr-relax.com/manual/frame_order_pdb_model.html frame_order.pdb_model user function].
* Created the Status_object.test_install_path system verification test. This is to catch bug #22037 ([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].
* Started to create a chapter for the N-state model or ensemble analysis in the manual. This simply consists of a few introductory sections and the phathalic acid graphic.
* Spacing improvements in the stereochem_analysis.py N-state mode sample script.
* Created the new [http://www.nmr-relax.com/manual/pymol_frame_order.html pymol.frame_order user function]. This user function pairs with the [http://www.nmr-relax.com/manual/frame_order_pdb_model.html frame_order.pdb_model user function], taking the three PDB files created and displaying them nicely. Neither user function is complete, however the rotor representation of certain frame order models is handled correctly.
* Created a script for finding all dead http://www.nmr-relax.com links in files of a directory tree.
* Created the Structure.test_bug_22041_atom_numbering system test to catch bug #22041. This was reported at [https://gna.org/bugs/?22041bug #22041]. The problem is that the [http://www.nmr-relax.com/manual/structure_write_pdb.html structure.write_pdb user function] does not create the correct atom serial numbers.
* Modified the [http://www.nmr-relax.com/manual/frame_order_pdb_model.html frame_order.pdb_model user function] so that the three PDB files are optional. This allows only certain components of the frame order theory to be represented in PDB format.
* Improvements for the rotor PDB representation shown by the [http://www.nmr-relax.com/manual/pymol_frame_order.html pymol.frame_order user function]. The stick radius width change is now only for the rotor PDB object, and not everything in PyMOL.
* The structure.read_* user function 'verbosity' argument is now passed into the structural object. This allows another printout to be silenced.
* The structure.read_* user function 'verbosity' argument is now passed into lib.io.open_read_file(). This allows all printouts from these three user functions to be suppressed.
* Converted the Mf.test_opendx_s2_te_rex system test into a GUI test. This is to demonstrate bug #22035 ([https://gna.org/bugs/?22035)bug #22035, the dx.map user function being broken in the GUI].
* Python 3 fixes for the extern.numpy_future module. These changes are necessary to allow relax to even run.
* Python 3 fixes for all of the relax code base. The lib.compat and multi.processor module changes were fatal, not useful for Python 3, and hence reverted.
== Bugfixes ==
* Fix for bug #21814 ([https://gna.org/bugs/?21814). This is bug #21814, the PDB reading failure when the PDB records are not padded to 80 spaces]. The fix is simple, all PDB records are pre-validated. This includes removing all newline characters and padding each PDB record to 80 spaces when needed. This will however add an overhead cost -- the internal PDB reader will now be slower. However corrupted PDB files, produced by MODELLER for example, not padded to 80 spaces will now be better supported.
* Bug fix for all of the R1rho relaxation dispersion models. The atan2() function is now being used rather than atan() for determining the rotating frame tilt angle. This is to allow the angle to be in the correct quadrant - i.e. to have a sign or direction.
* Huge speed up of the [http://www.nmr-relax.com/manual/interatom_define.html interatom.define user function]. This is to fix bug #21862 ([https://gna.org/bugs/?21862)bug #21862, the freezing up of relax when using the dipolar relaxation button in the model-free auto-analysis in the GUI]. This involves a number of changes. The algorithm for the backend of the interatom.define user function has been broken into two separate parts. The first part is new and uses the internal structural object atom_loop() twice for each spin ID string. This then calls the new are_bonded_index() structural object method which uses atom indices to find if two atoms are bonded, as the atom indices are returned from the atom_loop(). The are_bonded_index() is orders of magnitude faster than are_bonded() as selection objects are not used and the bonded data structure can be directly accessed. The are_bonded() method has also been slightly speed up by improving its logic. The second part is to perform the original algorithm of two nested spin loops over each spin ID and using the are_bonded() structural method. This second part only happens if the first part finds nothing. The structural object atom_loop() method has been modified to be able to return the molecule index. These indices are needed for the new are_bonded_index() method. When running relax with the profile flag turned on, a simple script which loads the 'Ubiquitin2.bz2' saved state and then the "interatom.define(spin_id1='@N', spin_id2='@H', direct_bond=True)" user function decreases from a total time of 143 to 3.8 seconds. However there are no speed changes detectable in the relax test suite - on one computer the system, unit and GUI tests only only vary by a fraction of a second.* Fix for the NOE analysis for the peak intensity parameters. This relates to bug #21863 ([https://gna.org/bugs/?21863)bug #21863, the grace.write user function not being able to write ref/sat plots as described in sample script noe.py]. The 'ref' and 'sat' parameters have been replaced by the 'intensities' dictionary data structure a long, long time ago. Therefore they have been eliminated and replaced by the 'intensities' definition.
* Fixes for the definitions of the N-state model analysis parameters. This analysis does not use the CSA value, and the paramagnetic centre is a list, not a float.
* Fixes for the definitions of the 'theta' and 'w_eff' relaxation dispersion parameters. These should not be manually changed by the user and they are not optimised parameter. Therefore they have been shifted from the set 'params' to the set 'all', to avoid listing them in the parameter tables (for example in the [http://www.nmr-relax.com/manual/value_set.html value.set user function]).
* Fixes for the [http://www.nmr-relax.com/manual/frame_order_pivot.html frame_order.pivot user function] - the model parameters were not being updated. The update_model() function is now called to make sure that the pivot point is either added or removed from the list of model parameters.
* Fix for bug #21924 ([https://gna.org/bugs/?21924). This is bug #21924, the failure to output 2D Grace plots for the R20, R20A, R20B, and R1rho0 relaxation dispersion parameters]. A simple test for missing data fixed the problem.* Fix for the Relax_disp.test_korzhnev_2005_15n_sq_data system test for certain MS Windows systems. This was reported as sr #3142 ([http://gna.org/support/?3142)sr #3142]. The problem was simply the lower precision of this system.* Fix for the cpmg_analysis.py relaxation dispersion sample script. This was reported as sr #3142 ([http://gna.org/support/?3142)sr #3142]. The problem was that one of the paths was in the Linux/Unix format and hence if the path is not changed by the user, then the script will not work for them if they are using MS Windows or Mac OS X.
* More path fixes for the sample scripts to allow them to run on MS Windows and Mac OS X. This is for the relaxation dispersion R1rho_analysis.py script and the N-state model conformation_analysis_rdc+pcs.py script. These scripts should be modified by the user for their own data, so they should not encounter this problem when using the scripts normally.
* Python 3 fixes throughout the codebase.
* 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 bug #21960 ([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 bug #21954, ([https://gna.org/bugs/?21954) - bug #21954, order of spectrum.error_analysis is important].* Fix for system test Relax_disp.test_hansen_cpmgfit_input. Bug #21989: ([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 "offset" and "point" swapped in looping. Bug #21989: ([https://gna.org/bugs/?21989) - Bug #21989, relax_disp.cpmgfit_input does not work for model CR72].* Fix for [https://gna.org/bugs/?21990 bug #21990, the --log and --tee options not functioning with the test suite. The bug report is at https://gna.org/bugs/?21990].* Fix for bug #21970 ([http://gna.org/bugs/?21970)bug #21970]. The Mac OS X dmg file required one of the test_suite/shared_data directories included in the 'include' list to properly bundle all relax modules inside the Mac App framework. This was achieved by creating a whitelist structure and adding the directory to that.* Fix for bug #21984 ([https://gna.org/bugs/?21984)bug #21984, the numpy.float16 error]. The numpy.float16 type is not defined for all numpy versions. Therefore the lib.check_types.float16 type is used instead as this defaults to numpy.float32 when numpy.float16 is missing.
* Fix for the [http://www.nmr-relax.com/manual/relax_disp_parameter_copy.html relax_disp.parameter_copy function]. The median of the values was not performed properly, since 0.0 was already in the starting list of values.
* Fix for the [http://www.nmr-relax.com/manual/relax_disp_parameter_copy.html relax_disp.parameter_copy user function] description. The parameters are not averaged but instead the median value from all spins is taken.
* Fix for [http://gna.org/bugs/?22001 bug #22001, the execution of script changing the current working directory. This is reported at http://gna.org/bugs/?22001]. The changing of the current working directory (CWD) was added to allow for nested scripting. However this is no longer needed as the script import mechanism has changed from the exec() function call to the runpy Python module.* Fix for [https://gna.org/bugs/?22002 bug #22002, the failure of the Library.test_library_independence software verification test. This is reported at https://gna.org/bugs/?22002]. The fix was simply to use the relax installation path in the status singleton object to make sure that the relax 'lib' directory can be found independently of what the current working directory is.
* Fix for path to sample data in sample script: sample_scripts/relax_disp/cpmg_analysis.py.
* Fix for path to sample data in sample script: sample_scripts/relax_disp/R1rho_analysis.py.
* Fix for [https://gna.org/bugs/?22004 bug #22004, the conformation_analysis_rdc+pcs.py N-state model sample script not working. This is reported at https://gna.org/bugs/?22004]. 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. Bug #22010 ([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.
* Fixed the rotor axis direction in the lib.frame_order.rotor_axis module. The normalisation code has also been simplified.
* Fix for tabular space and forgotten "\n" when writing dx.maps config files. Bug #22023: ([https://gna.org/bugs/?22023) Bug #22023: relax dx.map produce .net files which makes error].* 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 bug #21799 ([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 bug #21799 ([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. Bug #22019: ([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. Bug #22019: ([https://gna.org/bugs/?22019) Bug #22019: the IT99 model is listed with parameter kex instead of tex].* Small extra explanation in auto analysis. Bug #21799 ([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 bug #22037 ([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.
* Fixed the description of the N-state model in the [http://www.nmr-relax.com/manual/pipe_create.html pipe.create user function]. This has nothing to do with domain motions - it is the treatment of ensembles of structures.
* Fix for the axis labels in the [http://www.nmr-relax.com/manual/rdc_corr_plot.html rdc.corr_plot user function] when T data is converted to D.
* Fix for bug #22039, the printing out of Dpar twice by the diffusion_tensor.display user function. This is reported at https://gna.org/bugs/?22039. The solution is given in the original bug report.
* Fix for bug #22041, the PDB atom serial number error from the structure.write_pdb user function. This was reported at https://gna.org/bugs/?22041. The problem is that the [http://www.nmr-relax.com/manual/structure_write_pdb.html structure.write_pdb user function] preserves the atom numbering from the original structure and uses that for the atom serial number. However the atom serial number must be replaced with sequential values to produce a valid PDB file. This is fatal for any CONECT records.
* Fix for the chain-reaction failures in the test suite. This fixes bug #22055 ([https://gna.org/bugs/?22055)bug #22055, the processor.run_queue() not cleaning up in uni_processor - chain-reaction failures in the test suite]. The fix was insanely simple, just implementing what was mentioned Gary Thompson's FIXME comment in the run_queue() method of the uni-processor object. The queue execution code has been placed inside a 'try' statement and the queue cleaning up code in a 'finally' statement. This closes a painfully difficult to find bug that has been in relax since 2006, though only affecting relax developers.