From 56d9f7d28a6751b237f3a6b411b7bd429f579b5b Mon Sep 17 00:00:00 2001
From: Zhaoyi Shen <11598433+szy21@users.noreply.github.com>
Date: Wed, 27 Mar 2024 18:43:17 -0700
Subject: [PATCH 1/5] wip

---
 .buildkite/longruns/pipeline.yml              |  24 +--
 .buildkite/longruns_gpu/pipeline.yml          | 180 +-----------------
 ...equil_helem12_allsky_diagedmf_0M_earth.yml |  41 ++++
 ...lanet_equil_helem12_allsky_progedmf_0M.yml |  37 ++++
 ..._equil_helem12_allsky_progedmf_0M_asym.yml |  38 ++++
 ...equil_helem12_allsky_progedmf_0M_earth.yml |  44 +++++
 ...n_aquaplanet_equil_helem12_clearsky_0M.yml |  23 +++
 ...anet_equil_helem12_clearsky_0M_viscous.yml |  24 +++
 ...net_equil_helem12_clearsky_progedmf_0M.yml |  39 ++++
 ...quil_helem12_clearsky_progedmf_0M_asym.yml |  38 ++++
 ...e_equil_55km_nz63_clearsky_progedmf_0M.yml |  37 ++++
 .../prognostic_edmfx_adv_test_column.yml      |   4 +-
 .../prognostic_edmfx_aquaplanet.yml           |   7 +-
 .../prognostic_edmfx_trmm_column_0M.yml       |   4 +-
 post_processing/ci_plots.jl                   |   9 +-
 src/initial_conditions/initial_conditions.jl  |   9 +-
 src/prognostic_equations/edmfx_closures.jl    |   8 +
 src/prognostic_equations/edmfx_sgs_flux.jl    |   4 +
 src/prognostic_equations/hyperdiffusion.jl    |   2 +-
 ..._aquaplanet_equil_helem12_clearsky_0M.toml |  11 ++
 ...net_equil_helem12_clearsky_0M_viscous.toml |  14 ++
 ...et_equil_helem12_clearsky_diagedmf_0M.toml |  32 ++++
 ...et_equil_helem12_clearsky_progedmf_0M.toml |  50 +++++
 ..._equil_55km_nz63_clearsky_progedmf_0M.toml |   2 +-
 24 files changed, 478 insertions(+), 203 deletions(-)
 create mode 100644 config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_diagedmf_0M_earth.yml
 create mode 100644 config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_progedmf_0M.yml
 create mode 100644 config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_progedmf_0M_asym.yml
 create mode 100644 config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_progedmf_0M_earth.yml
 create mode 100644 config/longrun_configs/longrun_aquaplanet_equil_helem12_clearsky_0M.yml
 create mode 100644 config/longrun_configs/longrun_aquaplanet_equil_helem12_clearsky_0M_viscous.yml
 create mode 100644 config/longrun_configs/longrun_aquaplanet_equil_helem12_clearsky_progedmf_0M.yml
 create mode 100644 config/longrun_configs/longrun_aquaplanet_equil_helem12_clearsky_progedmf_0M_asym.yml
 create mode 100644 config/longrun_configs/longrun_aquaplanet_rhoe_equil_55km_nz63_clearsky_progedmf_0M.yml
 create mode 100644 toml/longrun_aquaplanet_equil_helem12_clearsky_0M.toml
 create mode 100644 toml/longrun_aquaplanet_equil_helem12_clearsky_0M_viscous.toml
 create mode 100644 toml/longrun_aquaplanet_equil_helem12_clearsky_diagedmf_0M.toml
 create mode 100644 toml/longrun_aquaplanet_equil_helem12_clearsky_progedmf_0M.toml

diff --git a/.buildkite/longruns/pipeline.yml b/.buildkite/longruns/pipeline.yml
index e131e2b493..b1f9cab81d 100644
--- a/.buildkite/longruns/pipeline.yml
+++ b/.buildkite/longruns/pipeline.yml
@@ -1,6 +1,5 @@
 agents:
   queue: new-central
-  slurm_mem_per_cpu: 8G
   modules: climacommon/2024_04_30
 
 env:
@@ -33,6 +32,7 @@ steps:
     agents:
       slurm_cpus_per_task: 8
       slurm_gpus: 1
+      slurm_ntasks: 1
     env:
       JULIA_NUM_PRECOMPILE_TASKS: 8
 
@@ -41,26 +41,14 @@ steps:
   - group: "Experimental long runs"
 
     steps:
-
-      # TODO: uncomment when zalesak works
-      # - label: ":computer: lim ARS zalesak baroclinic wave (ρe_tot) equilmoist high resolution"
-      #   command:
-      #     - srun julia --project=examples examples/hybrid/driver.jl --config_file $CONFIG_PATH/$$JOB_NAME.yml --job_id $$JOB_NAME
-      #   artifact_paths: "$$JOB_NAME/output_active/*"
-      #   agents:
-      #     slurm_ntasks: 32
-      #     slurm_mem_per_cpu: 32GB
-      #     slurm_time: 24:00:00
-      #   env:
-      #     JOB_NAME: "longrun_zalesak_tracer_energy_bw_rhoe_equil_highres"
-
-      - label: ":computer: SSP baroclinic wave (ρe_tot) equilmoist high resolution centered diff"
+      
+      - label: ":computer: aquaplanet equilmoist allsky radiation + prognostic edmf + 0M microphysics"
         command:
           - srun julia --project=examples examples/hybrid/driver.jl --config_file $CONFIG_PATH/$$JOB_NAME.yml --job_id $$JOB_NAME
         artifact_paths: "$$JOB_NAME/output_active/*"
         agents:
-          slurm_ntasks: 32
-          slurm_nodes: 2
+          slurm_gpus: 1
           slurm_time: 24:00:00
+          slurm_mem: 32GB
         env:
-          JOB_NAME: "longrun_ssp_bw_rhoe_equil_highres"
+          JOB_NAME: "longrun_aquaplanet_equil_helem12_allsky_progedmf_0M_earth"
diff --git a/.buildkite/longruns_gpu/pipeline.yml b/.buildkite/longruns_gpu/pipeline.yml
index a2e02ce751..f981456ee5 100644
--- a/.buildkite/longruns_gpu/pipeline.yml
+++ b/.buildkite/longruns_gpu/pipeline.yml
@@ -39,188 +39,16 @@ steps:
 
   - wait
 
-  - group: "helem 30 dycore"
-    steps:
-
-      - label: ":computer: hydrostatic balance (ρe_tot)"
-        command:
-          - srun julia --color=yes --project=examples examples/hybrid/driver.jl --config_file $CONFIG_PATH/$$JOB_NAME.yml --job_id $$JOB_NAME
-        artifact_paths: "$$JOB_NAME/output_active/*"
-        agents:
-          slurm_gpus: 1
-          slurm_time: 12:00:00
-        env:
-          JOB_NAME: "longrun_sphere_hydrostatic_balance_rhoe"
-
-      - label: ":computer: dry baroclinic wave"
-        command:
-          - srun julia --color=yes --project=examples examples/hybrid/driver.jl --config_file $CONFIG_PATH/$$JOB_NAME.yml --job_id $$JOB_NAME
-        artifact_paths: "$$JOB_NAME/output_active/*"
-        agents:
-          slurm_gpus: 1
-          slurm_time: 12:00:00
-        env:
-          JOB_NAME: "longrun_bw_rhoe_highres"
-
-      - label: ":computer: baroclinic wave equilmoist"
-        command:
-          - srun julia --color=yes --project=examples examples/hybrid/driver.jl --config_file $CONFIG_PATH/$$JOB_NAME.yml --job_id $$JOB_NAME
-        artifact_paths: "$$JOB_NAME/output_active/*"
-        agents:
-          slurm_gpus: 1
-          slurm_time: 12:00:00
-        env:
-          JOB_NAME: "longrun_bw_rhoe_equil_highres"
-
-      - label: ":computer: dry held-suarez"
-        command:
-          - srun julia --color=yes --project=examples examples/hybrid/driver.jl --config_file $CONFIG_PATH/$$JOB_NAME.yml --job_id $$JOB_NAME
-        artifact_paths: "$$JOB_NAME/output_active/*"
-        agents:
-          slurm_gpus: 1
-          slurm_time: 12:00:00
-        env:
-          JOB_NAME: "longrun_hs_rhoe_dry_55km_nz63"
-
-      - label: ":computer: held-suarez, equilmoist"
-        command:
-          - srun julia --color=yes --project=examples examples/hybrid/driver.jl --config_file $CONFIG_PATH/$$JOB_NAME.yml --job_id $$JOB_NAME
-        artifact_paths: "$$JOB_NAME/output_active/*"
-        agents:
-          slurm_gpus: 1
-          slurm_time: 12:00:00
-        env:
-          JOB_NAME: "longrun_hs_rhoe_equil_55km_nz63_0M"
-      
-      - label: ":computer: held-suarez equilmoist + deep-atmosphere eqns"
-        command:
-          - srun julia --color=yes --project=examples examples/hybrid/driver.jl --config_file $CONFIG_PATH/$$JOB_NAME.yml --job_id $$JOB_NAME
-        artifact_paths: "$$JOB_NAME/output_active/*"
-        env:
-          CLIMACORE_DISTRIBUTED: "MPI"
-          JOB_NAME: "longrun_hs_rhoe_equil_55km_nz63_0M_deepatmos"
-        agents:
-          slurm_gpus: 1
-          slurm_time: 12:00:00
-
   - group: "helem 16 aquaplanet"
     steps:
 
-      - label: ":computer: aquaplanet equilmoist gray radiation + 0M microphysics"
-        command:
-          - srun julia --color=yes --project=examples examples/hybrid/driver.jl --config_file $CONFIG_PATH/$$JOB_NAME.yml --job_id $$JOB_NAME
-        artifact_paths: "$$JOB_NAME/output_active/*"
-        env:
-          CLIMACORE_DISTRIBUTED: "MPI"
-          JOB_NAME: "longrun_aquaplanet_rhoe_equil_55km_nz63_gray_0M"
-        agents:
-          slurm_gpus: 1
-          slurm_time: 12:00:00
-
-      - label: ":computer: aquaplanet equilmoist clearsky radiation + 0M microphysics"
-        command:
-          - srun julia --color=yes --project=examples examples/hybrid/driver.jl --config_file $CONFIG_PATH/$$JOB_NAME.yml --job_id $$JOB_NAME
-        artifact_paths: "$$JOB_NAME/output_active/*"
-        agents:
-          slurm_gpus: 1
-          slurm_time: 12:00:00
-        env:
-          JOB_NAME: "longrun_aquaplanet_rhoe_equil_55km_nz63_clearsky_0M"
-
-      - label: ":computer: aquaplanet equilmoist clearsky radiation + diagnostic edmf + 0M microphysics"
-        command:
-          - srun julia --color=yes --project=examples examples/hybrid/driver.jl --config_file $CONFIG_PATH/$$JOB_NAME.yml --job_id $$JOB_NAME
-        artifact_paths: "$$JOB_NAME/output_active/*"
-        agents:
-          slurm_gpus: 1
-          slurm_time: 12:00:00
-        env:
-          JOB_NAME: "longrun_aquaplanet_rhoe_equil_55km_nz63_clearsky_diagedmf_0M"
-
-      - label: ":computer: aquaplanet equilmoist allsky radiation + diagnostic edmf + 0M microphysics"
-        command:
-          - srun julia --color=yes --project=examples examples/hybrid/driver.jl --config_file $CONFIG_PATH/$$JOB_NAME.yml --job_id $$JOB_NAME
-        artifact_paths: "$$JOB_NAME/output_active/*"
-        agents:
-          slurm_gpus: 1
-          slurm_time: 12:00:00
-        env:
-          JOB_NAME: "longrun_aquaplanet_rhoe_equil_55km_nz63_allsky_diagedmf_0M"
-
-        - label: ":computer: aquaplanet equilmoist clearsky radiation + prognostic edmf diffusion only + 0M microphysics"
+      - label: ":computer: aquaplanet equilmoist allsky radiation + prognostic edmf + 0M microphysics"
         command:
           - srun julia --project=examples examples/hybrid/driver.jl --config_file $CONFIG_PATH/$$JOB_NAME.yml --job_id $$JOB_NAME
         artifact_paths: "$$JOB_NAME/output_active/*"
         agents:
           slurm_gpus: 1
-          slurm_time: 12:00:00
-        env:
-          JOB_NAME: "longrun_aquaplanet_rhoe_equil_55km_nz63_clearsky_progedmf_diffonly_0M"
-
-      - label: ":computer: aquaplanet equilmoist clearsky radiation + 0M microphysics + earth topography"
-        command:
-          - srun julia --color=yes --project=examples examples/hybrid/driver.jl --config_file $CONFIG_PATH/$$JOB_NAME.yml --job_id $$JOB_NAME
-        artifact_paths: "$$JOB_NAME/output_active/*"
-        agents:
-          slurm_gpus: 1
-          slurm_time: 12:00:00
-        env:
-          JOB_NAME: "longrun_aquaplanet_rhoe_equil_55km_nz63_clearsky_0M_earth"
-
-      - label: ":computer: aquaplanet equilmoist clearsky radiation + 0M microphysics + earth topography (SLEVE)"
-        command:
-          - srun julia --color=yes --project=examples examples/hybrid/driver.jl --config_file $CONFIG_PATH/$$JOB_NAME.yml --job_id $$JOB_NAME
-        artifact_paths: "$$JOB_NAME/output_active/*"
-        agents:
-          slurm_gpus: 1
-          slurm_time: 6:00:00
-        env:
-          JOB_NAME: "longrun_aquaplanet_rhoe_equil_55km_nz63_clearsky_0M_earth_sleve"
-
-      - label: ":umbrella: aquaplanet equilmoist clearsky radiation + 1M microphysics"
-        command:
-          - srun julia --color=yes --project=examples examples/hybrid/driver.jl --config_file $CONFIG_PATH/$$JOB_NAME.yml --job_id $$JOB_NAME
-        artifact_paths: "$$JOB_NAME/output_active/*"
-        agents:
-          slurm_gpus: 1
-          slurm_time: 6:00:00
-        env:
-          JOB_NAME: "longrun_aquaplanet_clearsky_1M"
-
-      - label: ":computer: aquaplanet equilmoist clearsky radiation + time-varying insolation + 0M microphysics + slab ocean"
-        command:
-          - srun julia --color=yes --project=examples examples/hybrid/driver.jl --config_file $CONFIG_PATH/$$JOB_NAME.yml --job_id $$JOB_NAME
-        artifact_paths: "$$JOB_NAME/output_active/*"
-        agents:
-          slurm_gpus: 1
-          slurm_time: 12:00:00
-        env:
-          JOB_NAME: "longrun_aquaplanet_rhoe_equil_55km_nz63_clearsky_tvinsol_0M_slabocean"
-
-  - group: "DYAMOND"
-
-    steps:
-
-      - label: ":computer: aquaplanet dyamond"
-        command:
-          - srun julia --color=yes --project=examples examples/hybrid/driver.jl --config_file $CONFIG_PATH/$$JOB_NAME.yml --job_id $$JOB_NAME
-        artifact_paths: "$$JOB_NAME/output_active/*"
-        agents:
-          slurm_gpus: 1
-          slurm_time: 12:00:00
-        env:
-          JOB_NAME: "longrun_aquaplanet_dyamond"
-
-  - group: "atmos-only coupler runs"
-
-    steps:
-
-      - label: ":computer: amip target diagnostic edmf"
-        command:
-          - srun julia --color=yes --project=examples examples/hybrid/driver.jl --config_file $CONFIG_PATH/$$JOB_NAME.yml --job_id $$JOB_NAME
-        artifact_paths: "$$JOB_NAME/output_active/*"
-        agents:
-          slurm_gpus: 1
-          slurm_time: 12:00:00
+          slurm_time: 24:00:00
+          slurm_mem: 32GB
         env:
-          JOB_NAME: "amip_target_diagedmf"
+          JOB_NAME: "longrun_aquaplanet_equil_helem12_allsky_progedmf_0M_asym"
diff --git a/config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_diagedmf_0M_earth.yml b/config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_diagedmf_0M_earth.yml
new file mode 100644
index 0000000000..eed9627867
--- /dev/null
+++ b/config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_diagedmf_0M_earth.yml
@@ -0,0 +1,41 @@
+h_elem: 12
+z_max: 55000.0
+z_elem: 30
+dz_bottom: 100.0
+dz_top: 3000.0
+moist: "equil"
+precip_model: "0M"
+override_τ_precip: false
+rad: "allskywithclear"
+dt_rad: "6hours"
+surface_setup: "DefaultMoninObukhov"
+turbconv: "diagnostic_edmfx"
+implicit_diffusion: true
+approximate_linear_solve_iters: 2
+max_newton_iters_ode: 3
+prognostic_tke: true
+edmfx_upwinding: "first_order"
+edmfx_entr_model: "Generalized"
+edmfx_detr_model: "Generalized"
+edmfx_nh_pressure: true
+edmfx_sgs_mass_flux: true
+edmfx_sgs_diffusive_flux: true
+rayleigh_sponge: true
+vorticity_hyperdiffusion_coefficient: 1.0
+divergence_damping_factor: 4.0
+scalar_hyperdiffusion_coefficient: 4.0
+smoothing_order: 2
+topo_smoothing: true
+topography: "Earth"
+dt_save_state_to_disk: "10days"
+dt: "20secs"
+t_end: "2days"
+toml: [toml/longrun_aquaplanet_equil_helem12_clearsky_diagedmf_0M.toml]
+netcdf_output_at_levels: true
+diagnostics:
+  - short_name: [ts, ta, thetaa, ha, pfull, rhoa, ua, va, wa, hur, hus, cl, clw, cli, hussfc, evspsbl]
+    period: 1hours
+  - short_name: [arup, waup, rhoaup, taup, thetaaup, haup, husup, hurup, clwup, cliup, waen, tke]
+    period: 1hours
+  - short_name: [entr, detr, lmix, bgrad, strain, edt, evu]
+    period: 1hours
diff --git a/config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_progedmf_0M.yml b/config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_progedmf_0M.yml
new file mode 100644
index 0000000000..18f796a20a
--- /dev/null
+++ b/config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_progedmf_0M.yml
@@ -0,0 +1,37 @@
+h_elem: 12
+z_max: 55000.0
+z_elem: 35
+dz_bottom: 50.0
+dz_top: 3000.0
+moist: "equil"
+precip_model: "0M"
+override_τ_precip: false
+rad: "allskywithclear"
+dt_rad: "6hours"
+surface_setup: "DefaultMoninObukhov"
+turbconv: "prognostic_edmfx"
+implicit_sgs_advection: true
+implicit_diffusion: true
+approximate_linear_solve_iters: 2
+max_newton_iters_ode: 3
+prognostic_tke: true
+edmfx_upwinding: "first_order"
+edmfx_entr_model: "Generalized"
+edmfx_detr_model: "Generalized"
+edmfx_nh_pressure: true
+edmfx_filter: true
+edmfx_sgs_mass_flux: true
+edmfx_sgs_diffusive_flux: true
+rayleigh_sponge: true
+dt_save_state_to_disk: "10days"
+dt: "20secs"
+t_end: "30days"
+toml: [toml/longrun_aquaplanet_equil_helem12_clearsky_progedmf_0M.toml]
+netcdf_output_at_levels: true
+diagnostics:
+  - short_name: [ts, ta, thetaa, ha, pfull, rhoa, ua, va, wa, hur, hus, cl, clw, cli, hussfc, evspsbl]
+    period: 10days
+  - short_name: [arup, waup, rhoaup, taup, thetaaup, haup, husup, hurup, clwup, cliup, waen, taen, thetaaen, haen, husen, huren, clwen, clien, tke]
+    period: 10days
+  - short_name: [entr, detr, lmix, bgrad, strain, edt, evu]
+    period: 10days
diff --git a/config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_progedmf_0M_asym.yml b/config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_progedmf_0M_asym.yml
new file mode 100644
index 0000000000..309aac6a50
--- /dev/null
+++ b/config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_progedmf_0M_asym.yml
@@ -0,0 +1,38 @@
+h_elem: 12
+z_max: 55000.0
+z_elem: 35
+dz_bottom: 50.0
+dz_top: 3000.0
+moist: "equil"
+precip_model: "0M"
+override_τ_precip: false
+surface_temperature: "ZonallyAsymmetric"
+rad: "allskywithclear"
+dt_rad: "6hours"
+surface_setup: "DefaultMoninObukhov"
+turbconv: "prognostic_edmfx"
+implicit_sgs_advection: true
+implicit_diffusion: true
+approximate_linear_solve_iters: 2
+max_newton_iters_ode: 3
+prognostic_tke: true
+edmfx_upwinding: "first_order"
+edmfx_entr_model: "Generalized"
+edmfx_detr_model: "Generalized"
+edmfx_nh_pressure: true
+edmfx_filter: true
+edmfx_sgs_mass_flux: true
+edmfx_sgs_diffusive_flux: true
+rayleigh_sponge: true
+dt_save_state_to_disk: "10days"
+dt: "20secs"
+t_end: "30days"
+toml: [toml/longrun_aquaplanet_equil_helem12_clearsky_progedmf_0M.toml]
+netcdf_output_at_levels: true
+diagnostics:
+  - short_name: [ts, ta, thetaa, ha, pfull, rhoa, ua, va, wa, hur, hus, cl, clw, cli, hussfc, evspsbl]
+    period: 10days
+  - short_name: [arup, waup, rhoaup, taup, thetaaup, haup, husup, hurup, clwup, cliup, waen, taen, thetaaen, haen, husen, huren, clwen, clien, tke]
+    period: 10days
+  - short_name: [entr, detr, lmix, bgrad, strain, edt, evu]
+    period: 10days
diff --git a/config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_progedmf_0M_earth.yml b/config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_progedmf_0M_earth.yml
new file mode 100644
index 0000000000..dc473304ed
--- /dev/null
+++ b/config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_progedmf_0M_earth.yml
@@ -0,0 +1,44 @@
+h_elem: 12
+z_max: 55000.0
+z_elem: 30
+dz_bottom: 100.0
+dz_top: 3000.0
+moist: "equil"
+precip_model: "0M"
+override_τ_precip: false
+rad: "allskywithclear"
+dt_rad: "6hours"
+surface_setup: "DefaultMoninObukhov"
+turbconv: "prognostic_edmfx"
+implicit_sgs_advection: true
+implicit_diffusion: true
+approximate_linear_solve_iters: 2
+max_newton_iters_ode: 3
+prognostic_tke: true
+edmfx_upwinding: "first_order"
+edmfx_entr_model: "Generalized"
+edmfx_detr_model: "Generalized"
+edmfx_nh_pressure: true
+edmfx_filter: true
+edmfx_sgs_mass_flux: true
+edmfx_sgs_diffusive_flux: true
+rayleigh_sponge: true
+vorticity_hyperdiffusion_coefficient: 1.0
+divergence_damping_factor: 4.0
+scalar_hyperdiffusion_coefficient: 4.0
+smoothing_order: 2
+topo_smoothing: true
+topography: "Earth"
+dt_save_state_to_disk: "1days"
+dt: "20secs"
+t_end: "10days"
+restart_file: "/central/groups/esm/zhaoyi/climaatmos/longrun_1582/longrun_aquaplanet_equil_helem12_allsky_progedmf_0M_earth/output_active/day2.0.hdf5"
+toml: [toml/longrun_aquaplanet_equil_helem12_clearsky_progedmf_0M.toml]
+netcdf_output_at_levels: true
+diagnostics:
+  - short_name: [ts, ta, thetaa, ha, pfull, rhoa, ua, va, wa, hur, hus, cl, clw, cli, hussfc, evspsbl]
+    period: 1days
+  - short_name: [arup, waup, rhoaup, taup, thetaaup, haup, husup, hurup, clwup, cliup, waen, taen, thetaaen, haen, husen, huren, clwen, clien, tke]
+    period: 1days
+  - short_name: [entr, detr, lmix, bgrad, strain, edt, evu]
+    period: 1days
diff --git a/config/longrun_configs/longrun_aquaplanet_equil_helem12_clearsky_0M.yml b/config/longrun_configs/longrun_aquaplanet_equil_helem12_clearsky_0M.yml
new file mode 100644
index 0000000000..ad6b9145e2
--- /dev/null
+++ b/config/longrun_configs/longrun_aquaplanet_equil_helem12_clearsky_0M.yml
@@ -0,0 +1,23 @@
+h_elem: 12
+z_max: 55000.0
+z_elem: 30
+dz_bottom: 100.0
+dz_top: 3000.0
+moist: "equil"
+precip_model: "0M"
+override_τ_precip: false
+rad: "clearsky"
+dt_rad: "6hours"
+surface_setup: "DefaultMoninObukhov"
+vert_diff: "FriersonDiffusion"
+rayleigh_sponge: true
+dt_save_state_to_disk: "10days"
+dt: "200secs"
+t_end: "100days"
+toml: [toml/longrun_aquaplanet_equil_helem12_clearsky_0M.toml]
+netcdf_output_at_levels: true
+diagnostics:
+  - short_name: [ts, ta, thetaa, ha, pfull, rhoa, ua, va, wa, hur, hus, cl, clw, cli, hussfc, evspsbl]
+    period: 10days
+  - short_name: [lmix, bgrad, strain, edt, evu]
+    period: 10days
diff --git a/config/longrun_configs/longrun_aquaplanet_equil_helem12_clearsky_0M_viscous.yml b/config/longrun_configs/longrun_aquaplanet_equil_helem12_clearsky_0M_viscous.yml
new file mode 100644
index 0000000000..c63e5a810a
--- /dev/null
+++ b/config/longrun_configs/longrun_aquaplanet_equil_helem12_clearsky_0M_viscous.yml
@@ -0,0 +1,24 @@
+h_elem: 12
+z_max: 55000.0
+z_elem: 30
+dz_bottom: 100.0
+dz_top: 3000.0
+moist: "equil"
+precip_model: "0M"
+override_τ_precip: false
+rad: "clearsky"
+dt_rad: "6hours"
+surface_setup: "DefaultMoninObukhov"
+vert_diff: "FriersonDiffusion"
+rayleigh_sponge: true
+viscous_sponge: true
+dt_save_state_to_disk: "10days"
+dt: "200secs"
+t_end: "100days"
+toml: [toml/longrun_aquaplanet_equil_helem12_clearsky_0M_viscous.toml]
+netcdf_output_at_levels: true
+diagnostics:
+  - short_name: [ts, ta, thetaa, ha, pfull, rhoa, ua, va, wa, hur, hus, cl, clw, cli, hussfc, evspsbl]
+    period: 10days
+  - short_name: [lmix, bgrad, strain, edt, evu]
+    period: 10days
diff --git a/config/longrun_configs/longrun_aquaplanet_equil_helem12_clearsky_progedmf_0M.yml b/config/longrun_configs/longrun_aquaplanet_equil_helem12_clearsky_progedmf_0M.yml
new file mode 100644
index 0000000000..19300be151
--- /dev/null
+++ b/config/longrun_configs/longrun_aquaplanet_equil_helem12_clearsky_progedmf_0M.yml
@@ -0,0 +1,39 @@
+h_elem: 12
+z_max: 55000.0
+z_elem: 30
+dz_bottom: 100.0
+dz_top: 3000.0
+moist: "equil"
+precip_model: "0M"
+override_τ_precip: false
+rad: "clearsky"
+dt_rad: "6hours"
+surface_setup: "DefaultMoninObukhov"
+turbconv: "prognostic_edmfx"
+implicit_sgs_advection: true
+implicit_diffusion: true
+approximate_linear_solve_iters: 2
+max_newton_iters_ode: 3
+prognostic_tke: true
+edmfx_upwinding: "first_order"
+edmfx_entr_model: "Generalized"
+edmfx_detr_model: "Generalized"
+edmfx_nh_pressure: true
+edmfx_filter: true
+edmfx_sgs_mass_flux: true
+edmfx_sgs_diffusive_flux: true
+rayleigh_sponge: true
+viscous_sponge: true
+restart_file: "/central/groups/esm/zhaoyi/climaatmos/longrun_1560/longrun_aquaplanet_equil_helem12_clearsky_progedmf_0M/output_active/day30.0.hdf5"
+dt_save_state_to_disk: "10days"
+dt: "20secs"
+t_end: "32days"
+toml: [toml/longrun_aquaplanet_equil_helem12_clearsky_progedmf_0M.toml]
+netcdf_output_at_levels: true
+diagnostics:
+  - short_name: [ts, ta, thetaa, ha, pfull, rhoa, ua, va, wa, hur, hus, cl, clw, cli, hussfc, evspsbl]
+    period: 1days
+  - short_name: [arup, waup, rhoaup, taup, thetaaup, haup, husup, hurup, clwup, cliup, waen, taen, thetaaen, haen, husen, huren, clwen, clien, tke]
+    period: 1days
+  - short_name: [entr, detr, lmix, bgrad, strain, edt, evu]
+    period: 1days
diff --git a/config/longrun_configs/longrun_aquaplanet_equil_helem12_clearsky_progedmf_0M_asym.yml b/config/longrun_configs/longrun_aquaplanet_equil_helem12_clearsky_progedmf_0M_asym.yml
new file mode 100644
index 0000000000..4c92e1e960
--- /dev/null
+++ b/config/longrun_configs/longrun_aquaplanet_equil_helem12_clearsky_progedmf_0M_asym.yml
@@ -0,0 +1,38 @@
+h_elem: 12
+z_max: 55000.0
+z_elem: 30
+dz_bottom: 100.0
+dz_top: 3000.0
+moist: "equil"
+precip_model: "0M"
+override_τ_precip: false
+surface_temperature: "ZonallyAsymmetric"
+rad: "clearsky"
+dt_rad: "6hours"
+surface_setup: "DefaultMoninObukhov"
+turbconv: "prognostic_edmfx"
+implicit_sgs_advection: true
+implicit_diffusion: true
+approximate_linear_solve_iters: 2
+max_newton_iters_ode: 3
+prognostic_tke: true
+edmfx_upwinding: "first_order"
+edmfx_entr_model: "Generalized"
+edmfx_detr_model: "Generalized"
+edmfx_nh_pressure: true
+edmf_filter: true
+edmfx_sgs_mass_flux: true
+edmfx_sgs_diffusive_flux: true
+rayleigh_sponge: true
+dt_save_state_to_disk: "10days"
+dt: "40secs"
+t_end: "100days"
+toml: [toml/longrun_aquaplanet_rhoe_equil_55km_nz63_clearsky_progedmf_0M.toml]
+netcdf_output_at_levels: true
+diagnostics:
+  - short_name: [ts, ta, thetaa, ha, pfull, rhoa, ua, va, wa, hur, hus, cl, clw, cli, hussfc, evspsbl]
+    period: 10days
+  - short_name: [arup, waup, taup, thetaaup, haup, husup, hurup, clwup, cliup, waen, taen, thetaaen, haen, husen, huren, clwen, clien, tke]
+    period: 10days
+  - short_name: [entr, detr, lmix, bgrad, strain, edt, evu]
+    period: 10days
diff --git a/config/longrun_configs/longrun_aquaplanet_rhoe_equil_55km_nz63_clearsky_progedmf_0M.yml b/config/longrun_configs/longrun_aquaplanet_rhoe_equil_55km_nz63_clearsky_progedmf_0M.yml
new file mode 100644
index 0000000000..e9670daf50
--- /dev/null
+++ b/config/longrun_configs/longrun_aquaplanet_rhoe_equil_55km_nz63_clearsky_progedmf_0M.yml
@@ -0,0 +1,37 @@
+h_elem: 16
+z_max: 55000.0
+z_elem: 63
+dz_bottom: 30.0
+dz_top: 3000.0
+moist: "equil"
+precip_model: "0M"
+override_τ_precip: false
+rad: "clearsky"
+dt_rad: "6hours"
+surface_setup: "DefaultMoninObukhov"
+turbconv: "prognostic_edmfx"
+implicit_sgs_advection: true
+implicit_diffusion: true
+approximate_linear_solve_iters: 2
+max_newton_iters_ode: 3
+prognostic_tke: true
+edmfx_upwinding: "first_order"
+edmfx_entr_model: "Generalized"
+edmfx_detr_model: "Generalized"
+edmfx_nh_pressure: true
+edmf_filter: true
+edmfx_sgs_mass_flux: true
+edmfx_sgs_diffusive_flux: true
+rayleigh_sponge: true
+dt_save_state_to_disk: "3hours"
+dt: "40secs"
+t_end: "10days"
+toml: [toml/longrun_aquaplanet_rhoe_equil_55km_nz63_clearsky_progedmf_0M.toml]
+netcdf_output_at_levels: true
+diagnostics:
+  - short_name: [ts, ta, thetaa, ha, pfull, rhoa, ua, va, wa, hur, hus, cl, clw, cli, hussfc, evspsbl]
+    period: 1days
+  - short_name: [arup, waup, taup, thetaaup, haup, husup, hurup, clwup, cliup, waen, taen, thetaaen, haen, husen, huren, clwen, clien, tke]
+    period: 1days
+  - short_name: [entr, detr, lmix, bgrad, strain, edt, evu]
+    period: 1days
diff --git a/config/model_configs/prognostic_edmfx_adv_test_column.yml b/config/model_configs/prognostic_edmfx_adv_test_column.yml
index a53d91d1a5..c4856c8277 100644
--- a/config/model_configs/prognostic_edmfx_adv_test_column.yml
+++ b/config/model_configs/prognostic_edmfx_adv_test_column.yml
@@ -20,5 +20,7 @@ netcdf_interpolation_num_points: [2, 2, 63]
 diagnostics:
   - short_name: [ts, ta, thetaa, ha, pfull, rhoa, ua, va, wa, hur, hus, cl, clw, cli, hussfc, evspsbl]
     period: 10mins
-  - short_name: [arup, waup, taup, thetaaup, haup, husup, hurup, clwup, cliup, waen, taen, thetaaen, haen, husen, huren, clwen, clien, tke, lmix]
+  - short_name: [arup, waup, taup, thetaaup, haup, rhoaup, husup, hurup, clwup, cliup, waen, taen, thetaaen, haen, husen, huren, clwen, clien, tke, lmix]
+    period: 10mins
+  - short_name: [entr, detr, lmix, bgrad, strain, edt, evu]
     period: 10mins
diff --git a/config/model_configs/prognostic_edmfx_aquaplanet.yml b/config/model_configs/prognostic_edmfx_aquaplanet.yml
index f9895b9a0a..f25d36bfdd 100644
--- a/config/model_configs/prognostic_edmfx_aquaplanet.yml
+++ b/config/model_configs/prognostic_edmfx_aquaplanet.yml
@@ -17,9 +17,12 @@ dt_save_state_to_disk: 600secs
 toml: [toml/prognostic_edmfx.toml]
 output_default_diagnostics: false
 diagnostics:
-  - short_name: [ts, ta, thetaa, ha, pfull, rhoa, ua, va, wa, hfes, hur, hus, cl, clw, cli, evspsbl, rsd, rsu, rld, rlu]
+  - short_name: [ts, ta, thetaa, ha, pfull, rhoa, ua, va, wa, hur, hus, cl, clw, cli, hussfc, evspsbl]
     reduction_time: average
     period: 1hours
-  - short_name: [arup, waup, taup, thetaaup, haup, husup, hurup, clwup, cliup, waen, tke, lmix]
+  - short_name: [arup, waup, taup, thetaaup, haup, rhoaup, husup, hurup, clwup, cliup, waen, taen, thetaaen, haen, husen, huren, clwen, clien, tke, lmix]
+    reduction_time: average
+    period: 1hours
+  - short_name: [entr, detr, lmix, bgrad, strain, edt, evu]
     reduction_time: average
     period: 1hours
diff --git a/config/model_configs/prognostic_edmfx_trmm_column_0M.yml b/config/model_configs/prognostic_edmfx_trmm_column_0M.yml
index 384b2df555..443b18c8e0 100644
--- a/config/model_configs/prognostic_edmfx_trmm_column_0M.yml
+++ b/config/model_configs/prognostic_edmfx_trmm_column_0M.yml
@@ -31,5 +31,7 @@ netcdf_interpolation_num_points: [8, 8, 82]
 diagnostics:
   - short_name: [ts, ta, thetaa, ha, pfull, rhoa, ua, va, wa, hur, hus, cl, clw, cli, hussfc, evspsbl]
     period: 10mins
-  - short_name: [arup, waup, taup, thetaaup, haup, husup, hurup, clwup, cliup, waen, taen, thetaaen, haen, husen, huren, clwen, clien, tke, lmix]
+  - short_name: [arup, waup, taup, thetaaup, haup, husup, hurup, clwup, cliup, waen, taen, thetaaen, haen, husen, huren, clwen, clien, tke]
+    period: 10mins
+  - short_name: [entr, detr, lmix, bgrad, strain, edt, evu]
     period: 10mins
diff --git a/post_processing/ci_plots.jl b/post_processing/ci_plots.jl
index d4f73b3bd2..e1d613cff6 100644
--- a/post_processing/ci_plots.jl
+++ b/post_processing/ci_plots.jl
@@ -1135,8 +1135,6 @@ function make_plots(
         "cl",
         "clw",
         "clwup",
-        "cli",
-        "cliup",
         precip_names...,
     ]
     reduction = "inst"
@@ -1168,6 +1166,13 @@ function make_plots(
         ([slice(v, time = LAST_SNAP) for v in group]...,) for
         group in var_groups_zt
     ]
+    # var_groups_z = [
+    #     (
+    #         [
+    #             ClimaAnalysis.window(v, "time", left = 14400, right = 21600) |> ClimaAnalysis.average_time for v in group
+    #         ]...,
+    #     ) for group in var_groups_zt
+    # ]
 
     tmp_file = make_plots_generic(
         output_paths,
diff --git a/src/initial_conditions/initial_conditions.jl b/src/initial_conditions/initial_conditions.jl
index 87dced494b..94e30b861b 100644
--- a/src/initial_conditions/initial_conditions.jl
+++ b/src/initial_conditions/initial_conditions.jl
@@ -881,6 +881,13 @@ end
 The `InitialCondition` described in [Brown2002](@cite), but with a
 hydrostatically balanced pressure profile.
 """
+
+bomex_tke(::Type{FT}) where {FT} = z -> if (z <= 2500.0)
+    FT(1) - z / 3000
+else
+    FT(0)
+end
+
 Base.@kwdef struct ARM_SGP <: InitialCondition
     prognostic_tke::Bool = false
 end
@@ -918,7 +925,7 @@ for IC in (:Soares, :Bomex, :LifeCycleTan2018, :ARM_SGP)
                 ),
                 velocity = Geometry.UVector(u(z)),
                 turbconv_state = EDMFState(;
-                    tke = prognostic_tke ? FT(0) : tke(z),
+                    tke = prognostic_tke ? bomex_tke(FT)(z) : tke(z),
                 ),
             )
         end
diff --git a/src/prognostic_equations/edmfx_closures.jl b/src/prognostic_equations/edmfx_closures.jl
index 707b6ef28f..07b050bde1 100644
--- a/src/prognostic_equations/edmfx_closures.jl
+++ b/src/prognostic_equations/edmfx_closures.jl
@@ -242,9 +242,15 @@ function mixing_length(
         l_TKE > l_z ? l_z : l_TKE,
         l_W > l_z ? l_z : l_W,
     )
+    # l = SA.SVector(
+    #     (l_N < eps(FT) || l_N > l_z) ? l_z : l_N,
+    #     (l_TKE < eps(FT) || l_TKE > l_z) ? l_z : l_TKE,
+    #     (l_W < eps(FT) || l_W > l_z) ? l_z : l_W,
+    # )
     # get soft minimum
     l_smin = lamb_smooth_minimum(l, smin_ub, smin_rm)
     l_limited = max(l_smag, min(l_smin, l_z))
+    #l_limited = min(200, l_z)
 
     return MixingLength{FT}(l_limited, l_W, l_TKE, l_N)
 end
@@ -298,6 +304,8 @@ function edmfx_filter_tendency!(Yₜ, Y, p, t, turbconv_model::PrognosticEDMFX)
 
     n = n_mass_flux_subdomains(turbconv_model)
     (; dt) = p
+    (; ᶜK, ᶜh_tot, ᶜspecific, ᶜρa⁰, ᶜtke⁰) = p.precomputed
+    ᶜu₃ʲ = p.scratch.ᶜtemp_C3
 
     if p.atmos.edmfx_filter
         for j in 1:n
diff --git a/src/prognostic_equations/edmfx_sgs_flux.jl b/src/prognostic_equations/edmfx_sgs_flux.jl
index 3b3c2472b8..3ddbdae1d0 100644
--- a/src/prognostic_equations/edmfx_sgs_flux.jl
+++ b/src/prognostic_equations/edmfx_sgs_flux.jl
@@ -13,12 +13,16 @@ function edmfx_sgs_mass_flux_tendency!(
 )
 
     n = n_mass_flux_subdomains(turbconv_model)
+    turbconv_params = CAP.turbconv_params(p.params)
+    a_max = CAP.max_area(turbconv_params)
     (; edmfx_sgsflux_upwinding) = p.atmos.numerics
     (; ᶠu³, ᶜh_tot, ᶜspecific) = p.precomputed
     (; ᶠu³ʲs, ᶜKʲs, ᶜρʲs) = p.precomputed
     (; ᶜρa⁰, ᶜρ⁰, ᶠu³⁰, ᶜK⁰, ᶜmse⁰, ᶜq_tot⁰) = p.precomputed
     (; dt) = p
     ᶜJ = Fields.local_geometry_field(Y.c).J
+    FT = eltype(Y)
+    ᶜlg = Fields.local_geometry_field(Y.c)
 
     if p.atmos.edmfx_sgs_mass_flux
         # energy
diff --git a/src/prognostic_equations/hyperdiffusion.jl b/src/prognostic_equations/hyperdiffusion.jl
index cf046c05d9..e1d7d285bd 100644
--- a/src/prognostic_equations/hyperdiffusion.jl
+++ b/src/prognostic_equations/hyperdiffusion.jl
@@ -145,7 +145,7 @@ NVTX.@annotate function apply_hyperdiffusion_tendency!(Yₜ, Y, p, t)
 
     # Sub-grid scale hyperdiffusion continued
     if (turbconv_model isa PrognosticEDMFX) && diffuse_tke
-        @. Yₜ.c.sgs⁰.ρatke -= ν₄_vorticity * wdivₕ(ᶜρa⁰ * gradₕ(ᶜ∇²tke⁰))
+        @. Yₜ.c.sgs⁰.ρatke -= 4 * ν₄_vorticity * wdivₕ(ᶜρa⁰ * gradₕ(ᶜ∇²tke⁰))
     end
     if turbconv_model isa PrognosticEDMFX
         for j in 1:n
diff --git a/toml/longrun_aquaplanet_equil_helem12_clearsky_0M.toml b/toml/longrun_aquaplanet_equil_helem12_clearsky_0M.toml
new file mode 100644
index 0000000000..5697ca1f47
--- /dev/null
+++ b/toml/longrun_aquaplanet_equil_helem12_clearsky_0M.toml
@@ -0,0 +1,11 @@
+[zd_rayleigh]
+value = 35000.0
+
+[alpha_rayleigh_uh]
+value = 0.0
+
+[alpha_rayleigh_w]
+value = 10.0
+
+[precipitation_timescale]
+value = 600
diff --git a/toml/longrun_aquaplanet_equil_helem12_clearsky_0M_viscous.toml b/toml/longrun_aquaplanet_equil_helem12_clearsky_0M_viscous.toml
new file mode 100644
index 0000000000..76e5a39ca2
--- /dev/null
+++ b/toml/longrun_aquaplanet_equil_helem12_clearsky_0M_viscous.toml
@@ -0,0 +1,14 @@
+[zd_rayleigh]
+value = 35000.0
+
+[alpha_rayleigh_uh]
+value = 0.0
+
+[zd_viscous]
+value = 35000.0
+
+[kappa_2_sponge]
+value = 4e6
+
+[precipitation_timescale]
+value = 600
diff --git a/toml/longrun_aquaplanet_equil_helem12_clearsky_diagedmf_0M.toml b/toml/longrun_aquaplanet_equil_helem12_clearsky_diagedmf_0M.toml
new file mode 100644
index 0000000000..0151753122
--- /dev/null
+++ b/toml/longrun_aquaplanet_equil_helem12_clearsky_diagedmf_0M.toml
@@ -0,0 +1,32 @@
+[zd_rayleigh]
+value = 35000.0
+
+[alpha_rayleigh_uh]
+value = 0.0
+
+[alpha_rayleigh_w]
+value = 10.0
+
+[precipitation_timescale]
+value = 600
+
+[entr_inv_tau]
+value = 0.002
+
+[entr_coeff]
+value = 0
+
+[detr_inv_tau]
+value = 0
+
+[detr_buoy_coeff]
+value = 0.12
+
+[detr_vertdiv_coeff]
+value = 0
+
+[min_area_limiter_scale]
+value = 0
+
+[max_area_limiter_scale]
+value = 0
diff --git a/toml/longrun_aquaplanet_equil_helem12_clearsky_progedmf_0M.toml b/toml/longrun_aquaplanet_equil_helem12_clearsky_progedmf_0M.toml
new file mode 100644
index 0000000000..37497a5404
--- /dev/null
+++ b/toml/longrun_aquaplanet_equil_helem12_clearsky_progedmf_0M.toml
@@ -0,0 +1,50 @@
+[zd_rayleigh]
+value = 35000.0
+
+[alpha_rayleigh_uh]
+value = 0.0
+
+[alpha_rayleigh_w]
+value = 10.0
+
+[precipitation_timescale]
+value = 600
+
+[EDMF_surface_area]
+value = 0.1
+
+[EDMF_min_area]
+value = 1.0e-5
+
+[EDMF_max_area]
+value = 0.7
+
+[entr_inv_tau]
+value = 0.0002
+
+[entr_coeff]
+value = 0.2
+
+[min_area_limiter_scale]
+value = 0
+
+[min_area_limiter_power]
+value = 100
+
+[detr_inv_tau]
+value = 0
+
+[detr_coeff]
+value = 0
+
+[detr_buoy_coeff]
+value = 0
+
+[detr_vertdiv_coeff]
+value = 0
+
+[detr_massflux_vertdiv_coeff]
+value = 1
+
+[pressure_normalmode_drag_coeff]
+value = 40.0
diff --git a/toml/longrun_aquaplanet_rhoe_equil_55km_nz63_clearsky_progedmf_0M.toml b/toml/longrun_aquaplanet_rhoe_equil_55km_nz63_clearsky_progedmf_0M.toml
index c78bc0e113..c76bd0e1e8 100644
--- a/toml/longrun_aquaplanet_rhoe_equil_55km_nz63_clearsky_progedmf_0M.toml
+++ b/toml/longrun_aquaplanet_rhoe_equil_55km_nz63_clearsky_progedmf_0M.toml
@@ -8,7 +8,7 @@ value = 0.0
 value = 600
 
 [EDMF_surface_area]
-value = 0
+value = 0.1
 
 [EDMF_min_area]
 value = 1.0e-5

From 810184dace497d10eceac1ae395c694026ccd853 Mon Sep 17 00:00:00 2001
From: Zhaoyi Shen <11598433+szy21@users.noreply.github.com>
Date: Mon, 20 May 2024 17:17:35 -0700
Subject: [PATCH 2/5] restart

---
 ...planet_equil_helem12_allsky_progedmf_0M_asym.yml | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_progedmf_0M_asym.yml b/config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_progedmf_0M_asym.yml
index 309aac6a50..3037e8c4a1 100644
--- a/config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_progedmf_0M_asym.yml
+++ b/config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_progedmf_0M_asym.yml
@@ -24,15 +24,12 @@ edmfx_filter: true
 edmfx_sgs_mass_flux: true
 edmfx_sgs_diffusive_flux: true
 rayleigh_sponge: true
-dt_save_state_to_disk: "10days"
+dt_save_state_to_disk: "30days"
 dt: "20secs"
-t_end: "30days"
+t_end: "180days"
+restart_file: "/net/sampo/data1/zhaoyi/climaatmos/longrun_155/longrun_aquaplanet_equil_helem12_allsky_progedmf_0M_asym/output_active/day120.0.hdf5"
 toml: [toml/longrun_aquaplanet_equil_helem12_clearsky_progedmf_0M.toml]
 netcdf_output_at_levels: true
 diagnostics:
-  - short_name: [ts, ta, thetaa, ha, pfull, rhoa, ua, va, wa, hur, hus, cl, clw, cli, hussfc, evspsbl]
-    period: 10days
-  - short_name: [arup, waup, rhoaup, taup, thetaaup, haup, husup, hurup, clwup, cliup, waen, taen, thetaaen, haen, husen, huren, clwen, clien, tke]
-    period: 10days
-  - short_name: [entr, detr, lmix, bgrad, strain, edt, evu]
-    period: 10days
+  - short_name: [arup, waup, tke]
+    period: 30days

From 7b8d3456e0ab49433f81b809f980a42643471ffa Mon Sep 17 00:00:00 2001
From: Zhaoyi Shen <11598433+szy21@users.noreply.github.com>
Date: Mon, 27 May 2024 11:56:11 -0400
Subject: [PATCH 3/5] low res diagedmf

---
 .buildkite/longruns_gpu/pipeline.yml          |  4 +--
 ..._equil_helem12_allsky_diagedmf_0M_asym.yml | 32 +++++++++++++++++++
 2 files changed, 34 insertions(+), 2 deletions(-)
 create mode 100644 config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_diagedmf_0M_asym.yml

diff --git a/.buildkite/longruns_gpu/pipeline.yml b/.buildkite/longruns_gpu/pipeline.yml
index f981456ee5..a3703801ea 100644
--- a/.buildkite/longruns_gpu/pipeline.yml
+++ b/.buildkite/longruns_gpu/pipeline.yml
@@ -42,7 +42,7 @@ steps:
   - group: "helem 16 aquaplanet"
     steps:
 
-      - label: ":computer: aquaplanet equilmoist allsky radiation + prognostic edmf + 0M microphysics"
+      - label: ":computer: aquaplanet equilmoist allsky radiation + diagnostic edmf + 0M microphysics"
         command:
           - srun julia --project=examples examples/hybrid/driver.jl --config_file $CONFIG_PATH/$$JOB_NAME.yml --job_id $$JOB_NAME
         artifact_paths: "$$JOB_NAME/output_active/*"
@@ -51,4 +51,4 @@ steps:
           slurm_time: 24:00:00
           slurm_mem: 32GB
         env:
-          JOB_NAME: "longrun_aquaplanet_equil_helem12_allsky_progedmf_0M_asym"
+          JOB_NAME: "longrun_aquaplanet_equil_helem12_allsky_diagedmf_0M_asym"
diff --git a/config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_diagedmf_0M_asym.yml b/config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_diagedmf_0M_asym.yml
new file mode 100644
index 0000000000..143cc7051f
--- /dev/null
+++ b/config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_diagedmf_0M_asym.yml
@@ -0,0 +1,32 @@
+h_elem: 12
+z_max: 55000.0
+z_elem: 35
+dz_bottom: 50.0
+dz_top: 3000.0
+moist: "equil"
+precip_model: "0M"
+override_τ_precip: false
+surface_temperature: "ZonallyAsymmetric"
+rad: "allskywithclear"
+dt_rad: "6hours"
+surface_setup: "DefaultMoninObukhov"
+turbconv: "prognostic_edmfx"
+turbconv: "diagnostic_edmfx"
+implicit_diffusion: true
+approximate_linear_solve_iters: 2
+prognostic_tke: true
+edmfx_upwinding: "first_order"
+edmfx_entr_model: "Generalized"
+edmfx_detr_model: "Generalized"
+edmfx_nh_pressure: true
+edmfx_sgs_mass_flux: true
+edmfx_sgs_diffusive_flux: true
+rayleigh_sponge: true
+dt_save_state_to_disk: "30days"
+dt: "200secs"
+t_end: "180days"
+toml: [toml/longrun_aquaplanet_equil_helem12_clearsky_diagedmf_0M.toml]
+netcdf_output_at_levels: true
+diagnostics:
+  - short_name: [arup, waup, tke]
+    period: 30days

From 17da77a5d4ff0796cbf03860938bbbefc52fc5eb Mon Sep 17 00:00:00 2001
From: Zhaoyi Shen <11598433+szy21@users.noreply.github.com>
Date: Mon, 27 May 2024 15:19:52 -0400
Subject: [PATCH 4/5] restart progedmf

---
 .buildkite/longruns_gpu/pipeline.yml                          | 4 ++--
 ...ngrun_aquaplanet_equil_helem12_allsky_progedmf_0M_asym.yml | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.buildkite/longruns_gpu/pipeline.yml b/.buildkite/longruns_gpu/pipeline.yml
index a3703801ea..f981456ee5 100644
--- a/.buildkite/longruns_gpu/pipeline.yml
+++ b/.buildkite/longruns_gpu/pipeline.yml
@@ -42,7 +42,7 @@ steps:
   - group: "helem 16 aquaplanet"
     steps:
 
-      - label: ":computer: aquaplanet equilmoist allsky radiation + diagnostic edmf + 0M microphysics"
+      - label: ":computer: aquaplanet equilmoist allsky radiation + prognostic edmf + 0M microphysics"
         command:
           - srun julia --project=examples examples/hybrid/driver.jl --config_file $CONFIG_PATH/$$JOB_NAME.yml --job_id $$JOB_NAME
         artifact_paths: "$$JOB_NAME/output_active/*"
@@ -51,4 +51,4 @@ steps:
           slurm_time: 24:00:00
           slurm_mem: 32GB
         env:
-          JOB_NAME: "longrun_aquaplanet_equil_helem12_allsky_diagedmf_0M_asym"
+          JOB_NAME: "longrun_aquaplanet_equil_helem12_allsky_progedmf_0M_asym"
diff --git a/config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_progedmf_0M_asym.yml b/config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_progedmf_0M_asym.yml
index 3037e8c4a1..3b24915360 100644
--- a/config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_progedmf_0M_asym.yml
+++ b/config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_progedmf_0M_asym.yml
@@ -26,8 +26,8 @@ edmfx_sgs_diffusive_flux: true
 rayleigh_sponge: true
 dt_save_state_to_disk: "30days"
 dt: "20secs"
-t_end: "180days"
-restart_file: "/net/sampo/data1/zhaoyi/climaatmos/longrun_155/longrun_aquaplanet_equil_helem12_allsky_progedmf_0M_asym/output_active/day120.0.hdf5"
+t_end: "270days"
+restart_file: "/net/sampo/data1/zhaoyi/climaatmos/longrun_157/longrun_aquaplanet_equil_helem12_allsky_progedmf_0M_asym/output_active/day180.0.hdf5"
 toml: [toml/longrun_aquaplanet_equil_helem12_clearsky_progedmf_0M.toml]
 netcdf_output_at_levels: true
 diagnostics:

From 73cc90172d3617ec1702be2dde6a772cdd7130da Mon Sep 17 00:00:00 2001
From: Zhaoyi Shen <11598433+szy21@users.noreply.github.com>
Date: Tue, 28 May 2024 16:57:48 -0400
Subject: [PATCH 5/5] restart diagedmf and change parameters

---
 .buildkite/longruns_gpu/pipeline.yml                          | 4 ++--
 ...ngrun_aquaplanet_equil_helem12_allsky_diagedmf_0M_asym.yml | 3 ++-
 post_processing/ci_plots.jl                                   | 3 +++
 toml/diagnostic_edmfx.toml                                    | 2 +-
 4 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/.buildkite/longruns_gpu/pipeline.yml b/.buildkite/longruns_gpu/pipeline.yml
index f981456ee5..a3703801ea 100644
--- a/.buildkite/longruns_gpu/pipeline.yml
+++ b/.buildkite/longruns_gpu/pipeline.yml
@@ -42,7 +42,7 @@ steps:
   - group: "helem 16 aquaplanet"
     steps:
 
-      - label: ":computer: aquaplanet equilmoist allsky radiation + prognostic edmf + 0M microphysics"
+      - label: ":computer: aquaplanet equilmoist allsky radiation + diagnostic edmf + 0M microphysics"
         command:
           - srun julia --project=examples examples/hybrid/driver.jl --config_file $CONFIG_PATH/$$JOB_NAME.yml --job_id $$JOB_NAME
         artifact_paths: "$$JOB_NAME/output_active/*"
@@ -51,4 +51,4 @@ steps:
           slurm_time: 24:00:00
           slurm_mem: 32GB
         env:
-          JOB_NAME: "longrun_aquaplanet_equil_helem12_allsky_progedmf_0M_asym"
+          JOB_NAME: "longrun_aquaplanet_equil_helem12_allsky_diagedmf_0M_asym"
diff --git a/config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_diagedmf_0M_asym.yml b/config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_diagedmf_0M_asym.yml
index 143cc7051f..6c003e8059 100644
--- a/config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_diagedmf_0M_asym.yml
+++ b/config/longrun_configs/longrun_aquaplanet_equil_helem12_allsky_diagedmf_0M_asym.yml
@@ -24,7 +24,8 @@ edmfx_sgs_diffusive_flux: true
 rayleigh_sponge: true
 dt_save_state_to_disk: "30days"
 dt: "200secs"
-t_end: "180days"
+t_end: "270days"
+restart_file: "/net/sampo/data1/zhaoyi/climaatmos/longrun_160/longrun_aquaplanet_equil_helem12_allsky_diagedmf_0M_asym/output_active/day180.0.hdf5"
 toml: [toml/longrun_aquaplanet_equil_helem12_clearsky_diagedmf_0M.toml]
 netcdf_output_at_levels: true
 diagnostics:
diff --git a/post_processing/ci_plots.jl b/post_processing/ci_plots.jl
index e1d613cff6..2bba9f2326 100644
--- a/post_processing/ci_plots.jl
+++ b/post_processing/ci_plots.jl
@@ -1007,8 +1007,10 @@ end
 EDMFBoxPlots = Union{
     Val{:diagnostic_edmfx_gabls_box},
     Val{:diagnostic_edmfx_bomex_box},
+    Val{:diagnostic_edmfx_bomex_column},
     Val{:diagnostic_edmfx_bomex_stretched_box},
     Val{:diagnostic_edmfx_dycoms_rf01_box},
+    Val{:diagnostic_edmfx_dycoms_rf01_column},
     Val{:diagnostic_edmfx_trmm_box_0M},
     Val{:diagnostic_edmfx_dycoms_rf01_explicit_box},
     Val{:prognostic_edmfx_adv_test_column},
@@ -1030,6 +1032,7 @@ EDMFBoxPlotsWithPrecip = Union{
     Val{:prognostic_edmfx_trmm_column},
     Val{:diagnostic_edmfx_rico_box},
     Val{:diagnostic_edmfx_trmm_box},
+    Val{:diagnostic_edmfx_trmm_column},
     Val{:diagnostic_edmfx_trmm_stretched_box},
 }
 
diff --git a/toml/diagnostic_edmfx.toml b/toml/diagnostic_edmfx.toml
index 41c7c57094..860aec81e9 100644
--- a/toml/diagnostic_edmfx.toml
+++ b/toml/diagnostic_edmfx.toml
@@ -1,5 +1,5 @@
 [entr_inv_tau]
-value = 0.002
+value = 0.0015
 
 [entr_coeff]
 value = 0