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per-column inputs in JAX microphysics (#1407) * Align JAX microphysics with per-column Fortran inputs Pass each column’s parameters into PDF preparation and its own grid spacing into hydrometeor hole filling after the master multi-column fix. 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Both documentation skills validate, and relative-link checks pass. 2026-10-20 21:22:23 -050082c8fdb39580f015d26f9cb021b8376696d96b7fFix per-column inputs in JAX microphysics (#1407)editclubb_jax/src/Microphys/pdf_hydromet_microphys_wrapper.pyedit.agents/skills/clubb-documentation/change-messages/SKILL.mdeditclubb_jax/src/CLUBB_core/fill_holes.pyedit.agents/skills/clubb-documentation/language/SKILL.mdaddclubb_jax/pytests/auto_llm_generated_pytests/test_multicolumn_microphys_adapters.pygithttps://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreplyfalseStarted by user Gunther HueblerhueblerGunther 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differentiable legacy mixing length and migrate its selector (#1408) * Make legacy mixing length differentiable and migrate its selector The value-dependent JAX parcel loops prevented reverse differentiation and serialized independent launches. Use fixed scans with masks, batched launch levels and per-column error state while preserving Fortran stopping rules. Port the remaining legacy/tau branches and use the configured method in driver derivative checks. Replace the logical tau switch with Lscale_method (1=legacy, 2=tau), and rename mu to Lscale_mu_entrain throughout core, bindings, inputs and validation. Keep 102 tunable parameters; coherent physics is a separate follow-up. Local GNU Debug/API build, source checks, 447 unit checks and 240 API checks pass. Integrated Jenkins validation follows this checkpoint. * Read renamed entrainment parameters in Dash trajectories Saved output now names parcel entrainment Lscale_mu_entrain. Prefer that parameter while retaining support for older files saved with mu. Update Dash test settings to use the integer mixing-length selector. The local Dash suite passes 552 checks. * Require completed tests before branch finalization Requests to finalize immediately still require applicable Jenkins jobs to finish and their results to be reviewed. Distinguish validation checkpoints from a completed handoff, and report relevant stages of baseline-failing jobs. 2026-10-21 15:34:50 -0500dfa3b53697658b3f5f24cb5ae83c8e11fe0c0d65Port differentiable legacy mixing length and migrate its selector (#1408)editclubb_python_api/f2py_fortran_wrappers/model_flags_wrapper.F90editsrc/CLUBB_core/model_flags.F90editinput/flag_sets/run_bindiff_w_flags_config_core_flags.jsoneditclubb_jax/src/CLUBB_core/advance_clubb_core_module.pyedit.agents/skills/clubb-finalization/SKILL.mdeditinput/parameter_and_flag_configs/compatible_r8029/configurable_model_flags.ineditsrc/CLUBB_core/mixing_length.F90editsrc/CLUBB_core/parameter_indices.F90editclubb_jax/src/CLUBB_core/mixing_length.pyeditinput/parameter_and_flag_configs/coriolis_cases/ekman_parameters.ineditclubb_jax/src/CLUBB_core/model_flags.pyeditinput/parameter_and_flag_configs/tauMatchLscale/tunable_parameters.ineditinput/parameter_and_flag_configs/Lscale/tunable_parameters.ineditsrc/CLUBB_core/advance_clubb_core_module.F90editclubb_jax/src/CLUBB_core/numerical_check.pyeditclubb_jax/tests/run_jax_timestep_gradient_test.pyeditinput/parameter_and_flag_configs/tauMatchLscale/configurable_model_flags.ineditdash_app/pytests/test_callbacks_runs.pyedittests/run_python_vs_fortran_cases.pyeditclubb_jax/src/CLUBB_core/parameter_indices.pyeditclubb_jax/tests/test_loss_driver.pyeditdash_app/misc_tab/mixing_length_trajectories/analysis.pyedittests/run_jax_vs_fortran_cases.pyeditclubb_python_api/clubb_f2py.pyfeditinput/parameter_and_flag_configs/e3sm_maint32/tunable_parameters.ineditsrc/CLUBB_core/clubb_api_module.F90addclubb_jax/tests/benchmark_mixing_length.pyeditclubb_python_api/clubb_python/CLUBB_core/mixing_length.pyeditinput/parameter_and_flag_configs/coriolis_cases/atex_long_parameters.ineditinput/parameter_and_flag_configs/e3sm/tunable_parameters.ineditinput/parameter_and_flag_configs/coriolis_cases/coriolis_test_parameters.ineditsrc/G_unit_test_types/pdf_parameter_tests.F90editclubb_python_api/clubb_python/derived_types/config_flags_converter.pyeditsrc/clubb_driver.F90editclubb_jax/src/CLUBB_core/parameters_tunable.pyeditsrc/CLUBB_core/numerical_check.F90editclubb_python_driver/advance_clubb_core.pyeditclubb_python_driver/clubb_constants.pyeditinput/parameter_and_flag_configs/default/tunable_parameters.inedittuner/pytests/test_parameter_ranges.pyeditclubb_python_api/pytests/auto_llm_generated_pytests/test_init_sequence.pyeditclubb_jax/README.mdeditinput/parameter_and_flag_configs/e3sm/configurable_model_flags.ineditclubb_python_api/f2py_fortran_wrappers/mixing_length_wrapper.F90addclubb_jax/pytests/auto_llm_generated_pytests/test_mixing_length.pyeditdash_app/pytests/test_tune_callbacks_settings.pyeditclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_mixing_length_vs_fortran.pyeditclubb_python_api/pytests/auto_llm_generated_pytests/test_python_port_api_coverage.pyeditutilities/clubb_settings_validation.pyeditclubb_python_api/pytests/auto_llm_generated_pytests/test_call_tree_mixing_length.pyeditdash_app/pytests/test_run_runtime.pyeditsrc/clubb_tuner.F90editsrc/G_unit_test_types/spurious_source_test.F90editinput/parameter_and_flag_configs/Lscale/configurable_model_flags.inedittuner/pytests/test_adam_baselines.pyeditsrc/CLUBB_core/parameters_tunable.F90editsrc/SILHS/silhs_importance_sample_module.F90editclubb_jax/src/CLUBB_core/config_flags.pyeditclubb_python_api/clubb_python/derived_types/config_flags.pyeditinput/parameter_and_flag_configs/default/configurable_model_flags.ineditinput/parameter_and_flag_configs/e3sm_maint32/configurable_model_flags.ineditinput/flag_sets/config_core_flags_wo_never_supported_jax_features.jsoneditinput/parameter_and_flag_configs/e3sm_maint32/maint32_defaults_report.mdeditinput/parameter_and_flag_configs/compatible_r8029/tunable_parameters.inedittests/pytests/test_run_clubb_conv_test.pyeditutilities/pytests/test_settings_rules.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_param_names.pyeditinput/flag_sets/run_bindiff_w_flags_config_host_flags.jsoneditclubb_python_api/pytests/auto_llm_generated_pytests/test_call_tree_advance_xm_wpxp.pyedit.agents/skills/clubb-testing-and-reporting/SKILL.mdREADMEb2a6a9ceab12125d4a2542da4e20736039f3a7441792615282000https://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerhuebler@uwm.eduThe previous commit changed flags, which will now break the BFB tests even when the bit changing message is included, so now we need to have RESOLVED:dfa3b53697658b3f5f24cb5ae83c8e11fe0c0d65 messsages or enable temporary backwards compatibility. 2026-10-21 15:41:22 -0500b2a6a9ceab12125d4a2542da4e20736039f3a744The previous commit changed flags, which will now break the BFB tests even when the bit changing message is included, so now we need to have RESOLVED:dfa3b53697658b3f5f24cb5ae83c8e11fe0c0d65 messsages or enable temporary backwards compatibility.editREADMEgithttps://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerhttps://carson.math.uwm.edu/jenkins/user/noreplynoreplyfalse17https://carson.math.uwm.edu/jenkins/job/clubb_cmake/17/Started by an SCM change0001617736631665579893110.31674337440168369512fcc6487603491e12ac13376de2aec2a0b8369512fcc6487603491e12ac13376de2aec2a0brefs/remotes/origin/master8369512fcc6487603491e12ac13376de2aec2a0b8369512fcc6487603491e12ac13376de2aec2a0brefs/remotes/origin/master8369512fcc6487603491e12ac13376de2aec2a0b8369512fcc6487603491e12ac13376de2aec2a0brefs/remotes/origin/masterhttps://github.com/larson-group/clubb.gitfalse#1631665571792316clubb_cmake #1616false1611181SUCCESS1792486090432https://carson.math.uwm.edu/jenkins/job/clubb_cmake/16/src/generalized_grid_test.F90src/CLUBB_core/setup_clubb_pdf_params.F90clubb_python_api/clubb_f2py.pyfsrc/CLUBB_core/fill_holes.F90clubb_python_api/pytests/auto_llm_generated_pytests/test_call_tree_precipitation_fraction.pysrc/G_unit_test_types/mu_sigma_hm_tests.F90clubb_python_api/f2py_fortran_wrappers/precipitation_fraction_wrapper.F90clubb_python_api/clubb_python/CLUBB_core/precipitation_fraction.pysrc/Microphys/pdf_hydromet_microphys_wrapper.F90src/CLUBB_core/precipitation_fraction.F908369512fcc6487603491e12ac13376de2aec2a0b1792463005000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comClubb params 1d to 2d fix (#1392) * Fix: clubb params is a shape (ngrdcol,nparams) that is passed into subroutines that expect a 1d array Also fixed dependent other places in code and changed the python api. This is BIT_CHANGING for multicol. If a 2d array is passed into a function that expects the arr to be 1d fortran just passes the first col of the arr. Therefore the changes dont affect single col runs. For multicol runs other indexing is needed * fill_holes_vertical_api expects the passed gr%dzt to have shape(ngrdcol,nz) but the code passes the whole gr%dzt array although each column is traversed one by one. So ngrdcol=1 is passed each time. No effect on single col, as with ngrdcol = 1, gr%dzt and gr%dzt(1:1,:) are the same. Affects multicol if l_hole_fill = .true. and the hydrometeor is a mixing ratio (name starts with r) and some value is actually negative Therefore BIT_CHANGING 2026-10-19 21:23:25 -05008369512fcc6487603491e12ac13376de2aec2a0bClubb params 1d to 2d fix (#1392)editsrc/CLUBB_core/setup_clubb_pdf_params.F90editclubb_python_api/clubb_python/CLUBB_core/precipitation_fraction.pyeditclubb_python_api/pytests/auto_llm_generated_pytests/test_call_tree_precipitation_fraction.pyeditsrc/generalized_grid_test.F90editsrc/G_unit_test_types/mu_sigma_hm_tests.F90editsrc/Microphys/pdf_hydromet_microphys_wrapper.F90editclubb_python_api/clubb_f2py.pyfeditsrc/CLUBB_core/precipitation_fraction.F90editclubb_python_api/f2py_fortran_wrappers/precipitation_fraction_wrapper.F90editsrc/CLUBB_core/fill_holes.F90githttps://carson.math.uwm.edu/jenkins/user/noreplynoreplyfalse17https://carson.math.uwm.edu/jenkins/job/clubb_cmake/17/15https://carson.math.uwm.edu/jenkins/job/clubb_cmake/15/