Hi, With this change, I have finally grouped all of the optimisation functions together in their own user function class. The user functions are now called minimise.calculate, minimise.grid_search, and minimise.execute. The grouping is necessary to simplify the menus in the GUI, as I will be adding new user functions as needed for implementing a zooming grid search algorithm. If you have better suggestions for the names of these user functions, all input would be welcome.
As this is a massive change, this will require a change in the relax minor version number. Therefore the code of this zooming_grid_search branch and the disp_spin_speed branch could possibly both be released together as relax 3.3.0. Regards, Edward On 16 July 2014 20:57, <[email protected]> wrote: > Author: bugman > Date: Wed Jul 16 20:57:03 2014 > New Revision: 24545 > > URL: http://svn.gna.org/viewcvs/relax?rev=24545&view=rev > Log: > Redesign of the optimisation user functions calculate, grid_search, and > minimise. > > In preparation for expanding the number of optimisation user functions, these > three current user > functions have been shifted into the new minimise user function class. The > calculate user function > is now accessed as minimise.calculate. The grid search as > minimise.grid_search. And minimisation > is via the minimise.execute user function. The icon used for the new user > function class is the > Rosenbrock function or the banana optimisation problem. > > As this is such a radical change, a huge number of changes in the relax > source code, the sample > scripts, the user manual, and the test suite were required. > > > Modified: > branches/zooming_grid_search/auto_analyses/dauvergne_protocol.py > branches/zooming_grid_search/auto_analyses/frame_order.py > branches/zooming_grid_search/auto_analyses/noe.py > branches/zooming_grid_search/auto_analyses/relax_disp.py > branches/zooming_grid_search/auto_analyses/relax_fit.py > branches/zooming_grid_search/auto_analyses/stereochem_analysis.py > branches/zooming_grid_search/devel_scripts/memory_leak_test_relax_fit.py > branches/zooming_grid_search/docs/latex/consistency_tests.tex > branches/zooming_grid_search/docs/latex/curvefit.tex > branches/zooming_grid_search/docs/latex/dispersion.tex > branches/zooming_grid_search/docs/latex/intro.tex > branches/zooming_grid_search/docs/latex/jw_mapping.tex > branches/zooming_grid_search/docs/latex/model-free.tex > branches/zooming_grid_search/docs/latex/noe.tex > branches/zooming_grid_search/docs/latex/optimisation.tex > branches/zooming_grid_search/docs/prompt_screenshot.txt > branches/zooming_grid_search/sample_scripts/consistency_tests.py > branches/zooming_grid_search/sample_scripts/jw_mapping.py > branches/zooming_grid_search/sample_scripts/model_free/cv.py > branches/zooming_grid_search/sample_scripts/model_free/diff_min.py > branches/zooming_grid_search/sample_scripts/model_free/mf_multimodel.py > branches/zooming_grid_search/sample_scripts/model_free/single_model.py > > branches/zooming_grid_search/sample_scripts/n_state_model/conformation_analysis_rdc+pcs.py > > branches/zooming_grid_search/sample_scripts/n_state_model/local_min_search.py > branches/zooming_grid_search/sample_scripts/n_state_model/two_domain.py > branches/zooming_grid_search/sample_scripts/noe.py > branches/zooming_grid_search/sample_scripts/relax_fit.py > > branches/zooming_grid_search/test_suite/shared_data/bruker_files/relax_fit.py > > branches/zooming_grid_search/test_suite/shared_data/bruker_files/relax_fit_pdc_err.py > > branches/zooming_grid_search/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/relax_results/solution_ns_r1rho_2site.py > > branches/zooming_grid_search/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/relax_results/solution_tp02.py > > branches/zooming_grid_search/test_suite/shared_data/dispersion/Hansen/relax_results/analysis_mmq_cr72.py > > branches/zooming_grid_search/test_suite/shared_data/dispersion/Korzhnev_et_al_2005/relax_results/1H_SQ_CPMG/optimise.py > > branches/zooming_grid_search/test_suite/shared_data/dispersion/Korzhnev_et_al_2005/relax_results/DQ_CPMG/optimise.py > > branches/zooming_grid_search/test_suite/shared_data/dispersion/Korzhnev_et_al_2005/relax_results/cpmg_fit_solution.py > > branches/zooming_grid_search/test_suite/shared_data/dispersion/Korzhnev_et_al_2005/relax_results/cpmg_fit_solution_cr72.py > > branches/zooming_grid_search/test_suite/shared_data/dispersion/Korzhnev_et_al_2005/relax_results/optimise_sq.py > > branches/zooming_grid_search/test_suite/shared_data/dispersion/bug_22146_unpacking_r2a_r2b_cluster/cpmg_synthetic.py > > branches/zooming_grid_search/test_suite/shared_data/dispersion/error_testing/simulation.py > > branches/zooming_grid_search/test_suite/shared_data/dispersion/lm63_3site/relax_results/relax_disp_manual.py > > branches/zooming_grid_search/test_suite/shared_data/dispersion/ns_mmq_3site/relax_results/solution.py > > branches/zooming_grid_search/test_suite/shared_data/dispersion/ns_mmq_3site_linear/relax_results/solution.py > > branches/zooming_grid_search/test_suite/shared_data/dispersion/ns_r1rho_3site/relax_results/solution.py > > branches/zooming_grid_search/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/relax_results/solution.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/free_rotor/frame_order.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/free_rotor/tensor_fit.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/free_rotor2/tensor_fit.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/tensor_fit.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/iso_cone/frame_order.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/iso_cone/tensor_fit.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/tensor_fit.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/tensor_fit.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/frame_order.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/tensor_fit.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/pseudo_ellipse/multi_processor_test.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/pseudo_ellipse/tensor_fit.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/tensor_fit.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_pseudo_ellipse.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/tensor_fit.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/tensor_fit.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/rigid/frame_order.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/rigid/tensor_fit.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/rotor/frame_order.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/rotor/tensor_fit.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/rotor2/frame_order.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/rotor2/pcs_only/frame_order.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/rotor2/tensor_fit.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/rotor_2_state/frame_order.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/cam/rotor_2_state/tensor_fit.py > > branches/zooming_grid_search/test_suite/shared_data/frame_order/displacements/rigid_test.py > > branches/zooming_grid_search/test_suite/shared_data/relaxation_data/white_noise/simulation.py > branches/zooming_grid_search/test_suite/system_tests/frame_order.py > branches/zooming_grid_search/test_suite/system_tests/model_free.py > branches/zooming_grid_search/test_suite/system_tests/n_state_model.py > branches/zooming_grid_search/test_suite/system_tests/noe.py > branches/zooming_grid_search/test_suite/system_tests/relax_disp.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/1UBQ_relax_fit.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/bug_17276_peak_lists.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/bug_20674_ct_analysis_failure.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/bug_20674_jw_mapping.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/consistency_tests.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/consistency_tests_calc_test.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/curve_fitting/bug_18789_no_grace_errors.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/curve_fitting/bug_19887_curvefit_fail.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/diff_tensor/tensor_opt.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/frame_order/cam/base_script.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/frame_order/opt_rigid_rand_rot.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/frame_order/rigid_test.py > branches/zooming_grid_search/test_suite/system_tests/scripts/jw_mapping.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/jw_mapping_calc_test.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/model_free/bug_15050.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/model_free/bug_18790_negative_error.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/model_free/bug_20683_bdc_inf_values.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/model_free/bug_21079_local_tm_global_selection.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/model_free/bugs_12582_12591_12607.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/model_free/omp_model_free.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/model_free/opt_tm_fns.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/model_free/tylers_peptide.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/n_state_model/5_state_xz.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/n_state_model/absolute_T.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/n_state_model/absolute_rdcs.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/n_state_model/absolute_rdcs_menthol.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/n_state_model/align_fit.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/n_state_model/dna_pcs_fit.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/n_state_model/frame_order_align_fit.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/n_state_model/missing_data_test.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/n_state_model/monte_carlo_testing.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/n_state_model/paramag_align_fit.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/n_state_model/phthalic_acid_noes.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/n_state_model/populations.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/n_state_model/pyrotartaric_anhydride.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/n_state_model/rdc_tensor.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/noe/bug_21562_noe_replicate_fail.py > branches/zooming_grid_search/test_suite/system_tests/scripts/noe/noe.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/peak_lists/ccpn_analysis.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/relax_disp/cpmg_synthetic.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/relax_disp/ns_mmq_3site.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/relax_disp/ns_mmq_3site_linear.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/relax_disp/ns_r1rho_3site.py > > branches/zooming_grid_search/test_suite/system_tests/scripts/relax_disp/ns_r1rho_3site_linear.py > branches/zooming_grid_search/test_suite/system_tests/scripts/relax_fit.py > > branches/zooming_grid_search/test_suite/unit_tests/_prompt/test_minimisation.py > > branches/zooming_grid_search/test_suite/unit_tests/_specific_analyses/_relax_disp/test_data.py > branches/zooming_grid_search/user_functions/minimisation.py > branches/zooming_grid_search/user_functions/monte_carlo.py > > [This mail would be too long, it was shortened to contain the URLs only.] > > Modified: branches/zooming_grid_search/auto_analyses/dauvergne_protocol.py > URL: > http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/auto_analyses/dauvergne_protocol.py?rev=24545&r1=24544&r2=24545&view=diff > > Modified: branches/zooming_grid_search/auto_analyses/frame_order.py > URL: > http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/auto_analyses/frame_order.py?rev=24545&r1=24544&r2=24545&view=diff > > Modified: branches/zooming_grid_search/auto_analyses/noe.py > URL: > http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/auto_analyses/noe.py?rev=24545&r1=24544&r2=24545&view=diff > > Modified: branches/zooming_grid_search/auto_analyses/relax_disp.py > URL: > http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/auto_analyses/relax_disp.py?rev=24545&r1=24544&r2=24545&view=diff > > Modified: branches/zooming_grid_search/auto_analyses/relax_fit.py > URL: > http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/auto_analyses/relax_fit.py?rev=24545&r1=24544&r2=24545&view=diff > > Modified: branches/zooming_grid_search/auto_analyses/stereochem_analysis.py > URL: > http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/auto_analyses/stereochem_analysis.py?rev=24545&r1=24544&r2=24545&view=diff > > Modified: > branches/zooming_grid_search/devel_scripts/memory_leak_test_relax_fit.py > URL: > http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/devel_scripts/memory_leak_test_relax_fit.py?rev=24545&r1=24544&r2=24545&view=diff > > Modified: branches/zooming_grid_search/docs/latex/consistency_tests.tex > URL: > http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/docs/latex/consistency_tests.tex?rev=24545&r1=24544&r2=24545&view=diff > > Modified: branches/zooming_grid_search/docs/latex/curvefit.tex > URL: > http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/docs/latex/curvefit.tex?rev=24545&r1=24544&r2=24545&view=diff > > Modified: branches/zooming_grid_search/docs/latex/dispersion.tex > URL: > http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/docs/latex/dispersion.tex?rev=24545&r1=24544&r2=24545&view=diff > > Modified: branches/zooming_grid_search/docs/latex/intro.tex > URL: > http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/docs/latex/intro.tex?rev=24545&r1=24544&r2=24545&view=diff > > Modified: branches/zooming_grid_search/docs/latex/jw_mapping.tex > URL: > http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/docs/latex/jw_mapping.tex?rev=24545&r1=24544&r2=24545&view=diff > > Modified: branches/zooming_grid_search/docs/latex/model-free.tex > URL: > http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/docs/latex/model-free.tex?rev=24545&r1=24544&r2=24545&view=diff > > Modified: branches/zooming_grid_search/docs/latex/noe.tex > URL: > http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/docs/latex/noe.tex?rev=24545&r1=24544&r2=24545&view=diff > > Modified: branches/zooming_grid_search/docs/latex/optimisation.tex > URL: > http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/docs/latex/optimisation.tex?rev=24545&r1=24544&r2=24545&view=diff > > Modified: branches/zooming_grid_search/docs/prompt_screenshot.txt > URL: > http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/docs/prompt_screenshot.txt?rev=24545&r1=24544&r2=24545&view=diff > > Modified: branches/zooming_grid_search/sample_scripts/consistency_tests.py > URL: > http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/sample_scripts/consistency_tests.py?rev=24545&r1=24544&r2=24545&view=diff > > Modified: branches/zooming_grid_search/sample_scripts/jw_mapping.py > URL: > http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/sample_scripts/jw_mapping.py?rev=24545&r1=24544&r2=24545&view=diff > > Modified: branches/zooming_grid_search/sample_scripts/model_free/cv.py > URL: > http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/sample_scripts/model_free/cv.py?rev=24545&r1=24544&r2=24545&view=diff > > Modified: branches/zooming_grid_search/sample_scripts/model_free/diff_min.py > URL: > http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/sample_scripts/model_free/diff_min.py?rev=24545&r1=24544&r2=24545&view=diff > > Modified: > branches/zooming_grid_search/sample_scripts/model_free/mf_multimodel.py > URL: > http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/sample_scripts/model_free/mf_multimodel.py?rev=24545&r1=24544&r2=24545&view=diff > > Modified: > branches/zooming_grid_search/sample_scripts/model_free/single_model.py > URL: > http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/sample_scripts/model_free/single_model.py?rev=24545&r1=24544&r2=24545&view=diff > > Modified: > branches/zooming_grid_search/sample_scripts/n_state_model/conformation_analysis_rdc+pcs.py > URL: > http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/sample_scripts/n_state_model/conformation_analysis_rdc%2Bpcs.py?rev=24545&r1=24544&r2=24545&view=diff > > Modified: > branches/zooming_grid_search/sample_scripts/n_state_model/local_min_search.py > URL: > http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/sample_scripts/n_state_model/local_min_search.py?rev=24545&r1=24544&r2=24545&view=diff > > Modified: > branches/zooming_grid_search/sample_scripts/n_state_model/two_domain.py > URL: > http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/sample_scripts/n_state_model/two_domain.py?rev=24545&r1=24544&r2=24545&view=diff > > Modified: branches/zooming_grid_search/sample_scripts/noe.py > URL: > http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/sample_scripts/noe.py?rev=24545&r1=24544&r2=24545&view=diff > > Modified: branches/zooming_grid_search/sample_scripts/relax_fit.py > URL: > http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/sample_scripts/relax_fit.py?rev=24545&r1=24544&r2=24545&view=diff > > Modified: > branches/zooming_grid_search/test_suite/shared_data/bruker_files/relax_fit.py > URL: > http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/test_suite/shared_data/bruker_files/relax_fit.py?rev=24545&r1=24544&r2=24545&view=diff > > Modified: > branches/zooming_grid_search/test_suite/shared_data/bruker_files/relax_fit_pdc_err.py > URL: > http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/test_suite/shared_data/bruker_files/relax_fit_pdc_err.py?rev=24545&r1=24544&r2=24545&view=diff > > Modified: > branches/zooming_grid_search/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/relax_results/solution_ns_r1rho_2site.py > URL: > http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/relax_results/solution_ns_r1rho_2site.py?rev=24545&r1=24544&r2=24545&view=diff > > > [... 318 lines stripped ...] > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-commits mailing list > [email protected] > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-commits _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To 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