From d8bf3039a4d456c5b29eda43b6e8c12c5d8f1536 Mon Sep 17 00:00:00 2001
From: Zhaoyi Shen <11598433+szy21@users.noreply.github.com>
Date: Mon, 16 Sep 2024 14:57:15 -0700
Subject: [PATCH] use a higher model top

---
 config/model_configs/diagnostic_edmfx_aquaplanet.yml |  9 ++++++---
 .../diagnostic_edmfx_aquaplanet_gpu.yml              |  6 ++++--
 config/model_configs/prognostic_edmfx_aquaplanet.yml | 10 +++++++---
 .../single_column_hydrostatic_balance_ft64.yml       |  3 ++-
 ...radiative_equilibrium_allsky_idealized_clouds.yml |  6 +++---
 .../single_column_radiative_equilibrium_clearsky.yml |  6 +++---
 ..._equilibrium_clearsky_prognostic_surface_temp.yml |  7 +++----
 .../single_column_radiative_equilibrium_gray.yml     |  6 +++---
 ...oe_equilmoist_allsky_gw_raw_zonallyasymmetric.yml |  6 +++---
 ...here_aquaplanet_rhoe_equilmoist_allsky_gw_res.yml |  8 ++++----
 .../sphere_aquaplanet_rhoe_nonequilmoist_allsky.yml  |  8 ++++----
 ...re_held_suarez_rhoe_equilmoist_hightop_sponge.yml | 12 ++++++------
 .../sphere_held_suarez_rhoe_hightop.yml              |  8 +++++---
 src/cache/tracer_cache.jl                            |  3 +++
 toml/diagnostic_edmfx.toml                           |  3 +++
 toml/prognostic_edmfx.toml                           |  3 +++
 toml/sphere_held_suarez.toml                         |  6 ++++++
 ...e_held_suarez_rhoe_equilmoist_hightop_sponge.toml |  6 ------
 18 files changed, 68 insertions(+), 48 deletions(-)
 create mode 100644 toml/sphere_held_suarez.toml
 delete mode 100644 toml/sphere_held_suarez_rhoe_equilmoist_hightop_sponge.toml

diff --git a/config/model_configs/diagnostic_edmfx_aquaplanet.yml b/config/model_configs/diagnostic_edmfx_aquaplanet.yml
index bbfb7c149a6..45f9791c1dd 100644
--- a/config/model_configs/diagnostic_edmfx_aquaplanet.yml
+++ b/config/model_configs/diagnostic_edmfx_aquaplanet.yml
@@ -1,3 +1,7 @@
+z_max: 75000.0
+z_elem: 31
+dz_bottom: 50.0
+rayleigh_sponge: true
 surface_setup: DefaultMoninObukhov
 rad: clearsky
 turbconv: diagnostic_edmfx
@@ -13,9 +17,8 @@ edmfx_sgs_diffusive_flux: true
 moist: equil
 cloud_model: "quadrature_sgs"
 precip_model: 1M
-dt: 100secs
-t_end: 12hours
-dt_save_state_to_disk: 12hours
+dt: 120secs
+t_end: 3hours
 regression_test: true
 toml: [toml/diagnostic_edmfx.toml]
 ode_algo: ARS343
diff --git a/config/model_configs/diagnostic_edmfx_aquaplanet_gpu.yml b/config/model_configs/diagnostic_edmfx_aquaplanet_gpu.yml
index f311520ea3d..f02270058fb 100644
--- a/config/model_configs/diagnostic_edmfx_aquaplanet_gpu.yml
+++ b/config/model_configs/diagnostic_edmfx_aquaplanet_gpu.yml
@@ -1,3 +1,6 @@
+z_max: 75000.0
+z_elem: 31
+dz_bottom: 50.0
 surface_setup: DefaultMoninObukhov
 rad: clearsky
 turbconv: diagnostic_edmfx
@@ -13,8 +16,7 @@ edmfx_sgs_diffusive_flux: true
 moist: equil
 cloud_model: "quadrature_sgs"
 precip_model: 1M
-dt: 100secs
+dt: 120secs
 t_end: 12hours
-dt_save_state_to_disk: 12hours
 toml: [toml/diagnostic_edmfx.toml]
 ode_algo: ARS343
diff --git a/config/model_configs/prognostic_edmfx_aquaplanet.yml b/config/model_configs/prognostic_edmfx_aquaplanet.yml
index 55268833026..2c99228d592 100644
--- a/config/model_configs/prognostic_edmfx_aquaplanet.yml
+++ b/config/model_configs/prognostic_edmfx_aquaplanet.yml
@@ -1,3 +1,7 @@
+z_max: 75000.0
+z_elem: 31
+dz_bottom: 50.0
+rayleigh_sponge: true
 surface_setup: DefaultMoninObukhov
 rad: clearsky
 turbconv: prognostic_edmfx
@@ -13,15 +17,15 @@ moist: equil
 cloud_model: "quadrature_sgs"
 precip_model: 1M
 dt: 10secs
-t_end: 1hours
+t_end: 1800secs
 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, pr, rsd, rsu, rld, rlu]
     reduction_time: average
-    period: 1hours
+    period: 1800secs
   - short_name: [arup, waup, taup, thetaaup, haup, husup, hurup, clwup, cliup, waen, tke, lmix]
     reduction_time: average
-    period: 1hours
+    period: 1800secs
 ode_algo: ARS343
diff --git a/config/model_configs/single_column_hydrostatic_balance_ft64.yml b/config/model_configs/single_column_hydrostatic_balance_ft64.yml
index 225a48d0600..9413a32114e 100644
--- a/config/model_configs/single_column_hydrostatic_balance_ft64.yml
+++ b/config/model_configs/single_column_hydrostatic_balance_ft64.yml
@@ -1,9 +1,10 @@
+z_max: 75000.0
+z_elem: 63
 dz_bottom: 30.0
 dt_save_state_to_disk: "5days"
 initial_condition: "IsothermalProfile"
 config: "column"
 hyperdiff: false
-z_elem: 45
 dt: "3hours"
 FLOAT_TYPE: "Float64"
 dt_save_to_sol: "3hours"
diff --git a/config/model_configs/single_column_radiative_equilibrium_allsky_idealized_clouds.yml b/config/model_configs/single_column_radiative_equilibrium_allsky_idealized_clouds.yml
index 10d5bc77b17..6eb27c4e967 100644
--- a/config/model_configs/single_column_radiative_equilibrium_allsky_idealized_clouds.yml
+++ b/config/model_configs/single_column_radiative_equilibrium_allsky_idealized_clouds.yml
@@ -1,16 +1,16 @@
+z_max: 75000.0
+z_elem: 63
+dz_bottom: 30.0
 dt_save_state_to_disk: "100days"
 initial_condition: "IsothermalProfile"
 hyperdiff: false
-z_elem: 63
 dt: "3hours"
 dt_rad: "3hours"
 idealized_h2o: true
 t_end: "654days"
 idealized_clouds: true
-dz_bottom: 30.0
 config: "column"
 insolation: "timevarying"
-z_max: 70000.0
 dt_save_to_sol: "30hours"
 rad: "allskywithclear"
 diagnostics:
diff --git a/config/model_configs/single_column_radiative_equilibrium_clearsky.yml b/config/model_configs/single_column_radiative_equilibrium_clearsky.yml
index f8b197d8060..5a10c450c94 100644
--- a/config/model_configs/single_column_radiative_equilibrium_clearsky.yml
+++ b/config/model_configs/single_column_radiative_equilibrium_clearsky.yml
@@ -1,13 +1,13 @@
+z_max: 75000.0
+z_elem: 63
+dz_bottom: 30.0
 dt_save_state_to_disk: "100days"
 initial_condition: "IsothermalProfile"
 hyperdiff: false
-z_elem: 63
 dt: "3hours"
 dt_rad: "3hours"
 idealized_h2o: true
 t_end: "654days"
-dz_bottom: 30.0
 config: "column"
-z_max: 70000.0
 dt_save_to_sol: "30hours"
 rad: "clearsky"
diff --git a/config/model_configs/single_column_radiative_equilibrium_clearsky_prognostic_surface_temp.yml b/config/model_configs/single_column_radiative_equilibrium_clearsky_prognostic_surface_temp.yml
index e49d6ec462f..97aa564b7b2 100644
--- a/config/model_configs/single_column_radiative_equilibrium_clearsky_prognostic_surface_temp.yml
+++ b/config/model_configs/single_column_radiative_equilibrium_clearsky_prognostic_surface_temp.yml
@@ -1,12 +1,11 @@
-
+z_max: 75000.0
+z_elem: 63
+dz_bottom: 30.0
 rad: "clearsky"
 idealized_h2o: true
 hyperdiff: false
 config: "column"
 initial_condition: "IsothermalProfile"
-z_max: 70000
-z_elem: 63
-dz_bottom: 30
 t_end: "654days"
 dt: "3hours"
 dt_rad: "3hours"
diff --git a/config/model_configs/single_column_radiative_equilibrium_gray.yml b/config/model_configs/single_column_radiative_equilibrium_gray.yml
index 02b096b8fa9..7e535965d1b 100644
--- a/config/model_configs/single_column_radiative_equilibrium_gray.yml
+++ b/config/model_configs/single_column_radiative_equilibrium_gray.yml
@@ -1,15 +1,15 @@
 dt_save_state_to_disk: "3months"
 initial_condition: "IsothermalProfile"
 hyperdiff: false
-# It seems radiative equilibrium needs a larger dz near the top
-# to be stable, so we use a smaller z_elem
+# It seems radiative equilibrium needs a lower top and a larger dz 
+# near the top (smaller z_elem) to be stable
+z_max: 70000.0
 z_elem: 50
 dt: "3hours"
 dt_rad: "3hours"
 t_end: "654days"
 dz_bottom: 30.0
 config: "column"
-z_max: 70000.0
 dt_save_to_sol: "30hours"
 rad: "gray"
 # [2, 2, 80] instead of [1, 1, 80] because Julia ranges are inclusive of the
diff --git a/config/model_configs/sphere_aquaplanet_rhoe_equilmoist_allsky_gw_raw_zonallyasymmetric.yml b/config/model_configs/sphere_aquaplanet_rhoe_equilmoist_allsky_gw_raw_zonallyasymmetric.yml
index 65097acad14..cd2b7a93e54 100644
--- a/config/model_configs/sphere_aquaplanet_rhoe_equilmoist_allsky_gw_raw_zonallyasymmetric.yml
+++ b/config/model_configs/sphere_aquaplanet_rhoe_equilmoist_allsky_gw_raw_zonallyasymmetric.yml
@@ -1,16 +1,16 @@
+z_max: 75000.0
+z_elem: 31
+dz_bottom: 50.0
 rad: "allskywithclear"
 dt_save_state_to_disk: "1days"
 rayleigh_sponge: true
 orographic_gravity_wave: "raw_topo"
-z_elem: 25
 dt: "400secs"
 surface_setup: "DefaultMoninObukhov"
 t_end: "15hours"
 non_orographic_gravity_wave: true
-dz_bottom: 300.0
 vert_diff: true
 insolation: "timevarying"
-z_max: 55000.0
 precip_model: "0M"
 cloud_model: "grid_scale"
 surface_temperature: "ZonallyAsymmetric"
diff --git a/config/model_configs/sphere_aquaplanet_rhoe_equilmoist_allsky_gw_res.yml b/config/model_configs/sphere_aquaplanet_rhoe_equilmoist_allsky_gw_res.yml
index 3ced2aaf4f2..6bfe271b73e 100644
--- a/config/model_configs/sphere_aquaplanet_rhoe_equilmoist_allsky_gw_res.yml
+++ b/config/model_configs/sphere_aquaplanet_rhoe_equilmoist_allsky_gw_res.yml
@@ -1,6 +1,6 @@
-z_elem: 25
-z_max: 55000.0
-dz_bottom: 300.0
+z_max: 75000.0
+z_elem: 31
+dz_bottom: 50.0
 dt: "400secs"
 t_end: "1days"
 dt_save_state_to_disk: "24hours"
@@ -18,7 +18,7 @@ orographic_gravity_wave: "gfdl_restart"
 surface_setup: "DefaultMoninObukhov"
 prescribe_ozone: true
 prescribed_aerosols: ["CB1", "CB2", "SO4"]
-toml: [toml/sphere_aquaplanet_rhoe_equilmoist_allsky_gw_res.toml]
+toml: [toml/sphere_held_suarez.toml]
 diagnostics:
   - short_name: [edt, evu, mmrso4, mmrbcpo, mmrbcpi, o3]
     reduction_time: average
diff --git a/config/model_configs/sphere_aquaplanet_rhoe_nonequilmoist_allsky.yml b/config/model_configs/sphere_aquaplanet_rhoe_nonequilmoist_allsky.yml
index 1fed54c9c3e..c5bb4fd7c08 100644
--- a/config/model_configs/sphere_aquaplanet_rhoe_nonequilmoist_allsky.yml
+++ b/config/model_configs/sphere_aquaplanet_rhoe_nonequilmoist_allsky.yml
@@ -1,6 +1,6 @@
-z_elem: 25
-z_max: 55000.0
-dz_bottom: 300.0
+z_max: 75000.0
+z_elem: 31
+dz_bottom: 50.0
 dt: "400secs"
 t_end: "18hours"
 dt_save_state_to_disk: "18hours"
@@ -14,4 +14,4 @@ rad: "allskywithclear"
 insolation: "timevarying"
 rayleigh_sponge: true
 surface_setup: "DefaultMoninObukhov"
-toml: [toml/sphere_aquaplanet_rhoe_equilmoist_allsky_gw_res.toml]
+toml: [toml/sphere_held_suarez.toml]
diff --git a/config/model_configs/sphere_held_suarez_rhoe_equilmoist_hightop_sponge.yml b/config/model_configs/sphere_held_suarez_rhoe_equilmoist_hightop_sponge.yml
index 685851fb0a7..fcf5ebc21da 100644
--- a/config/model_configs/sphere_held_suarez_rhoe_equilmoist_hightop_sponge.yml
+++ b/config/model_configs/sphere_held_suarez_rhoe_equilmoist_hightop_sponge.yml
@@ -1,14 +1,14 @@
+z_max: 75000.0
+z_elem: 31
+dz_bottom: 50.0
 dt_save_state_to_disk: "4days"
-rayleigh_sponge: true
-dt: "450secs"
-z_elem: 25
+dt: "400secs"
 t_end: "4days"
-dz_bottom: 300.0
 vert_diff: true
 forcing: "held_suarez"
-z_max: 55000.0
 precip_model: "0M"
 regression_test: true
+rayleigh_sponge: true
 viscous_sponge: true
 moist: "equil"
-toml: [toml/sphere_held_suarez_rhoe_equilmoist_hightop_sponge.toml]
+toml: [toml/sphere_held_suarez.toml]
diff --git a/config/model_configs/sphere_held_suarez_rhoe_hightop.yml b/config/model_configs/sphere_held_suarez_rhoe_hightop.yml
index 6e9f232f5b5..1913a3affea 100644
--- a/config/model_configs/sphere_held_suarez_rhoe_hightop.yml
+++ b/config/model_configs/sphere_held_suarez_rhoe_hightop.yml
@@ -1,8 +1,10 @@
-dz_bottom: 300.0
+z_max: 75000.0
+z_elem: 31
+dz_bottom: 50.0
 dt_save_state_to_disk: "4days"
 t_end: "8days"
 forcing: "held_suarez"
 dt: "400secs"
-z_elem: 25
 deep_atmosphere: true
-z_max: 55000.0
+rayleigh_sponge: true
+toml: [toml/sphere_held_suarez.toml]
diff --git a/src/cache/tracer_cache.jl b/src/cache/tracer_cache.jl
index 4b57ab75890..e03d8d714dc 100644
--- a/src/cache/tracer_cache.jl
+++ b/src/cache/tracer_cache.jl
@@ -2,6 +2,7 @@ using ClimaUtilities.ClimaArtifacts
 import Dates: Year
 import ClimaUtilities.TimeVaryingInputs:
     TimeVaryingInput, LinearPeriodFillingInterpolation
+import Interpolations as Intp
 
 function tracer_cache(
     Y,
@@ -47,6 +48,7 @@ function tracer_cache(
         # time series of lon-lat-z data.
         prescribed_aerosol_names_as_symbols = Symbol.(prescribed_aerosol_names)
         target_space = axes(Y.c)
+        extrapolation_bc = (Intp.Periodic(), Intp.Flat(), Intp.Flat())
         timevaryinginputs = [
             TimeVaryingInput(
                 joinpath(
@@ -60,6 +62,7 @@ function tracer_cache(
                 target_space;
                 reference_date = start_date,
                 regridder_type = :InterpolationsRegridder,
+                regridder_kwargs = (; extrapolation_bc),
                 method = LinearPeriodFillingInterpolation(Year(1)),
             ) for name in prescribed_aerosol_names
         ]
diff --git a/toml/diagnostic_edmfx.toml b/toml/diagnostic_edmfx.toml
index 41c7c570941..4e415a01fb7 100644
--- a/toml/diagnostic_edmfx.toml
+++ b/toml/diagnostic_edmfx.toml
@@ -1,3 +1,6 @@
+[zd_rayleigh]
+value = 50000.0
+
 [entr_inv_tau]
 value = 0.002
 
diff --git a/toml/prognostic_edmfx.toml b/toml/prognostic_edmfx.toml
index 654a543e810..9ba0a563786 100644
--- a/toml/prognostic_edmfx.toml
+++ b/toml/prognostic_edmfx.toml
@@ -22,6 +22,9 @@ value = 0
 [detr_coeff]
 value = 0
 
+[zd_rayleigh]
+value = 50000.0
+
 [detr_buoy_coeff]
 value = 0
 
diff --git a/toml/sphere_held_suarez.toml b/toml/sphere_held_suarez.toml
new file mode 100644
index 00000000000..46b16eedac7
--- /dev/null
+++ b/toml/sphere_held_suarez.toml
@@ -0,0 +1,6 @@
+[zd_viscous]
+value = 50000.0
+
+[zd_rayleigh]
+value = 50000.0
+
diff --git a/toml/sphere_held_suarez_rhoe_equilmoist_hightop_sponge.toml b/toml/sphere_held_suarez_rhoe_equilmoist_hightop_sponge.toml
deleted file mode 100644
index cda298c6791..00000000000
--- a/toml/sphere_held_suarez_rhoe_equilmoist_hightop_sponge.toml
+++ /dev/null
@@ -1,6 +0,0 @@
-[zd_viscous]
-value = 30000.0
-
-[zd_rayleigh]
-value = 30000.0
-