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Huebler</fullName></author><authorEmail>huebler@uwm.edu</authorEmail><comment>Archiving experimental files that were used to explore some crazy PDF diagnosis methods. Much of this is sporatic LLM generated code and reports. These two methods were tested and did work well when using LES input to model the PDF, but were extemely noisy and unstable in free running clubb. The 'parcel tracking' one performs a mixing-length-like calculation to evolve a persistent 3rd gaussian, then computes a residual ADG1 pair to balance everything out and adhere to clubbs predicted moments. The second one (dubbed trivariate even though they're technically all trivariate) is a 2 Gaussian method that allows for many more degrees of freedom in how we place Gaussian centers and allocate covariance - it does this in part by taking into account rt and thl skewness, which require calculating rtp3 and thlp3. This trivate actually does really well when modelled using LES data, but it's heavy reliance on xp3 terms makes it extremely noisy and bad in clubb - this is why this code also includes a much more sophisticated (and barely tested) advance_xp3_module.F90, as an attempt to make this less worse for the trivariate pdf.
</comment><date>2026-07-27 20:59:56 -0500</date><id>bf9986a7c169085e4f89733f84407bd222075934</id><msg>Archiving experimental files that were used to explore some crazy PDF diagnosis methods. Much of this is sporatic LLM generated code and reports. These two methods were tested and did work well when using LES input to model the PDF, but were extemely noisy and unstable in free running clubb. The 'parcel tracking' one performs a mixing-length-like calculation to evolve a persistent 3rd gaussian, then computes a residual ADG1 pair to balance everything out and adhere to clubbs predicted moments. The second one (dubbed trivariate even though they're technically all trivariate) is a 2 Gaussian method that allows for many more degrees of freedom in how we place Gaussian centers and allocate covariance - it does this in part by taking into account rt and thl skewness, which require calculating rtp3 and thlp3. This trivate actually does really well when modelled using LES data, but it's heavy reliance on xp3 terms makes it extremely noisy and bad in clubb - this is why this code also includes a much more sophisticated (and barely tested) advance_xp3_module.F90, as an attempt to make this less worse for the trivariate pdf.</msg><path><editType>add</editType><file>experimental/experimental_pdfs/python/dash_additions/misc_labs/tests/test_transport_2g_prototype.py</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/python/report_scripts/generate_pdf10_arm_noise_report.py</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/src/CLUBB_core/trivariate_transport_pdf.F90</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/python/report_scripts/directional_lscale_pdf_coherence/generate_report.py</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/python/dash_additions/misc_labs/tests/test_mixed_moment_allocation.py</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/python/dash_additions/misc_labs/__init__.py</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/python/report_scripts/pdf10_arm_xp3_budget_audit/generate_pdf10_arm_xp3_budget_report.py</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/python/dash_additions/misc_labs/tests/test_vertical_coherence.py</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/src/CLUBB_core/pdf_9_module.F90</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/python/dash_additions/misc_labs/trivariate_transport_sam_lab.py</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/python/dash_additions/misc_labs/vertically_coherent_transport_sam_lab.py</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/src/G_unit_test_types/trivariate_transport_pdf_tests.F90</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/python/dash_additions/misc_labs/transport_2g_prototype.py</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/python/dash_additions/misc_labs/vertical_coherence.py</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/doc/trivariate_transport_method_report.md</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/src/CLUBB_core/pdf_closure_module.F90</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/doc/pdf_method_investigation_report.md</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/python/dash_additions/misc_labs/pdf9_parcel_ensemble.py</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/python/dash_additions/src/pdf_9_module.F90</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/python/dash_additions/utilities/generate_pdf9_parcel_ensemble_diagnostics.py</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/python/dash_additions/misc_labs/sam_lscale.py</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/python/dash_additions/misc_labs/tests/test_pdf9_parcel_ensemble_report.py</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/README.md</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/python/report_scripts/pdf10_mixed_third_moment_decision/generate_report.py</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/python/dash_additions/misc_labs/tests/test_refresh_pdf9_parcel_ensemble_lab.py</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/python/report_scripts/pdf10_flux_alignment_effect/generate_report.py</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/python/dash_additions/utilities/refresh_pdf9_parcel_ensemble_lab.py</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/src/CLUBB_core/advance_xp3_module.F90</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/doc/vertically_coherent_pdf_diagnosis.md</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/python/report_scripts/pdf10_arm_scalar_third_moment_noise_audit/generate_pdf10_arm_noise_report.py</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/python/report_scripts/pdf10_arm_rt_thl_structure/generate_report.py</file></path><path><editType>add</editType><file>experimental/experimental_pdfs/python/report_scripts/generate_pdf10_arm_xp3_budget_report.py</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>src/CLUBB_core/advance_xp3_module.F90</affectedPath><commitId>765ae7c30cda88e01b27cd1ee4277d54e4fcb752</commitId><timestamp>1785204361000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/huebler</absoluteUrl><fullName>Gunther Huebler</fullName></author><authorEmail>huebler@uwm.edu</authorEmail><comment>Fixing bug in advance_xp3 code. This is BFB because advance_xp3 is hardcoded to false.
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</comment><date>2026-07-25 13:05:43 -0500</date><id>02babc6b5a46bda3075bf071426fa20bf200a43b</id><msg>Setting l_diag_Lscale_from_tau to false by default, and changing it to true in the flag set list the run_bindiff_w_flags test uses so that we keep testing the tau code nightly. This flag changes answers, so this is BIT_CHANGING.</msg><path><editType>edit</editType><file>input/flag_sets/run_bindiff_w_flags_config_core_flags.json</file></path><path><editType>edit</editType><file>src/CLUBB_core/model_flags.F90</file></path><path><editType>edit</editType><file>input/parameter_and_flag_configs/default/configurable_model_flags.in</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>tests/run_python_vs_fortran_cases.py</affectedPath><commitId>afbbe1126523c6ff7a4bb8091f72a242280490ba</commitId><timestamp>1785004898000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/huebler</absoluteUrl><fullName>Gunther Huebler</fullName></author><authorEmail>huebler@uwm.edu</authorEmail><comment>Setting l_diag_Lscale_from_tau to false caused dycoms2_rf01_fixed_sst to start failing the python vs fortran test. The differences were small and occured at a late timestep, so to fix the test I put a limiter on the number of timesteps the test runs.
</comment><date>2026-07-25 13:41:38 -0500</date><id>afbbe1126523c6ff7a4bb8091f72a242280490ba</id><msg>Setting l_diag_Lscale_from_tau to false caused dycoms2_rf01_fixed_sst to start failing the python vs fortran test. The differences were small and occured at a late timestep, so to fix the test I put a limiter on the number of timesteps the test runs.</msg><path><editType>edit</editType><file>tests/run_python_vs_fortran_cases.py</file></path></item><item 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.math.uwm.edu/jenkins/user/huebler</absoluteUrl><fullName>Gunther Huebler</fullName></author><authorEmail>huebler@uwm.edu</authorEmail><comment>Removing the l_tke_aniso flag
</comment><date>2026-07-25 13:44:53 -0500</date><id>8ab3902e812c2883976b4f1f57c085d682666d92</id><msg>Removing the l_tke_aniso flag</msg><path><editType>edit</editType><file>clubb_jax/clubb_case_initalization.py</file></path><path><editType>edit</editType><file>input/parameter_and_flag_configs/default/configurable_model_flags.in</file></path><path><editType>edit</editType><file>input/parameter_and_flag_configs/e3sm_maint32/configurable_model_flags.in</file></path><path><editType>edit</editType><file>src/G_unit_test_types/spurious_source_test.F90</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/clip_explicit.py</file></path><path><editType>edit</editType><file>clubb_python_api/f2py_fortran_wrappers/advance_wp2_wp3_module_wrapper.F90</file></path><path><editType>edit</editType><file>clubb_python_driver/clubb_case_initalization.py</file></path><path><editType>edit</editType><file>input/parameter_and_flag_configs/compatible_r8029/tunable_parameters.in</file></path><path><editType>edit</editType><file>input/parameter_and_flag_configs/e3sm_maint32/maint32_defaults_report.md</file></path><path><editType>edit</editType><file>src/CLUBB_core/advance_wp2_wp3_module.F90</file></path><path><editType>edit</editType><file>input/parameter_and_flag_configs/e3sm/configurable_model_flags.in</file></path><path><editType>edit</editType><file>input/parameter_and_flag_configs/Lscale/tunable_parameters.in</file></path><path><editType>edit</editType><file>src/CLUBB_core/constants_clubb.F90</file></path><path><editType>edit</editType><file>src/CLUBB_core/clip_explicit.F90</file></path><path><editType>edit</editType><file>input/parameter_and_flag_configs/Lscale/configurable_model_flags.in</file></path><path><editType>edit</editType><file>input/parameter_and_flag_configs/default/tunable_parameters.in</file></path><path><editType>edit</editType><file>clubb_jax/advance_clubb_core.py</file></path><path><editType>edit</editType><file>clubb_python_api/f2py_fortran_wrappers/advance_windm_edsclrm_module_wrapper.F90</file></path><path><editType>edit</editType><file>input/case_setups/dycoms2_rf02_ds_model.LR.in</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/advance_windm_edsclrm.py</file></path><path><editType>edit</editType><file>src/Microphys/pdf_hydromet_microphys_wrapper.F90</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/derived_types/config_flags.py</file></path><path><editType>edit</editType><file>input/case_setups/dycoms2_rf02_so_model.HR.in</file></path><path><editType>edit</editType><file>input/case_setups/dycoms2_rf02_ds_model.HR.in</file></path><path><editType>edit</editType><file>input/case_setups/dycoms2_rf02_nd_model.LR.in</file></path><path><editType>edit</editType><file>input/parameter_and_flag_configs/coriolis_cases/atex_long_parameters.in</file></path><path><editType>edit</editType><file>input/parameter_and_flag_configs/e3sm/tunable_parameters.in</file></path><path><editType>edit</editType><file>input/parameter_and_flag_configs/compatible_r8029/configurable_model_flags.in</file></path><path><editType>edit</editType><file>src/G_unit_test_types/pdf_parameter_tests.F90</file></path><path><editType>edit</editType><file>clubb_python_driver/advance_clubb_core.py</file></path><path><editType>edit</editType><file>src/clubb_tuner.F90</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_advance_wp2_wp3.py</file></path><path><editType>edit</editType><file>input/case_setups/dycoms2_rf02_so_model.LR.in</file></path><path><editType>edit</editType><file>input/case_setups/README</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/advance_xm_wpxp.py</file></path><path><editType>edit</editType><file>src/CLUBB_core/advance_windm_edsclrm_module.F90</file></path><path><editType>edit</editType><file>input/parameter_and_flag_configs/tauMatchLscale/configurable_model_flags.in</file></path><path><editType>edit</editType><file>src/clubb_driver.F90</file></path><path><editType>edit</editType><file>src/CLUBB_core/advance_clubb_core_module.F90</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_init_sequence.py</file></path><path><editType>edit</editType><file>input/parameter_and_flag_configs/coriolis_cases/ekman_parameters.in</file></path><path><editType>edit</editType><file>input/flag_sets/run_bindiff_w_flags_config_core_flags.json</file></path><path><editType>edit</editType><file>clubb_python_api/f2py_fortran_wrappers/clip_explicit_wrapper.F90</file></path><path><editType>edit</editType><file>clubb_python_api/f2py_fortran_wrappers/advance_xm_wpxp_module_wrapper.F90</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/advance_wp2_wp3.py</file></path><path><editType>edit</editType><file>clubb_python_api/f2py_fortran_wrappers/model_flags_wrapper.F90</file></path><path><editType>edit</editType><file>input/flag_sets/run_bindiff_w_flags_config_host_flags.json</file></path><path><editType>edit</editType><file>clubb_python_api/club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