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, <edward@xxxxxxxxxxxxx> 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 ...]
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Renaming of the calc, grid_search, and minimise user functions.