Fix Deardorff overwrite of theta_v component. (#1641)

* Fix Deardorff overwrite of theta_v component.

* fix indentation.

* fix logic error.

Exec/DevTests/Bomex/input_Kessler

@@ -0,0 +1,100 @@
+# ------------------  INPUTS TO MAIN PROGRAM  -------------------
+stop_time = 43200
+
+amrex.fpe_trap_invalid = 1
+
+fabarray.mfiter_tile_size = 1024 1024 1024
+
+# PROBLEM SIZE & GEOMETRY
+geometry.prob_extent =  3200     3200    4000
+amr.n_cell           =    32       32     100
+
+geometry.is_periodic = 1 1 0
+
+# MOST BOUNDARY (DEFAULT IS ADIABATIC FOR THETA)
+zlo.type = "Most"
+erf.most.flux_type = "custom"
+erf.most.ustar  = 0.28   # ustar
+erf.most.tstar  = 8.0e-3 # theta flux
+erf.most.qstar  = 5.2e-5 # qv    flux
+erf.most.z0     = 0.1
+erf.most.zref   = 20.0
+
+// NOTE: This should have a qv grad too (use hoextrapcc?!)
+zhi.type = "SlipWall"
+zhi.theta_grad = 0.00365
+
+# TIME STEP CONTROL
+erf.fixed_dt       = 0.5 # fixed time step depending on grid resolution
+
+# DIAGNOSTICS & VERBOSITY
+erf.sum_interval   = 1       # timesteps between computing mass
+erf.v              = 1       # verbosity in ERF.cpp
+amr.v              = 1       # verbosity in Amr.cpp
+erf.data_log       = "surf" "mean" "flux" "subgrid"
+erf.profile_int    = 120 
+
+# REFINEMENT / REGRIDDING
+amr.max_level       = 0       # maximum level number allowed
+
+# CHECKPOINT FILES
+erf.check_file      = chk        # root name of checkpoint file
+erf.check_int       = 600        # number of timesteps between checkpoints
+
+# PLOTFILES
+erf.plot_file_1     = plt       # prefix of plotfile name
+erf.plot_int_1      = 120        # number of timesteps between plotfiles
+erf.plot_vars_1     = density rhotheta x_velocity y_velocity z_velocity pressure temp theta qt qp qv qc qi
+
+# SOLVER CHOICE
+erf.alpha_T = 0.0
+erf.alpha_C = 0.0
+erf.use_gravity = true
+
+erf.dycore_horiz_adv_type    = Upwind_5th
+erf.dycore_vert_adv_type     = Upwind_5th
+erf.dryscal_horiz_adv_type   = WENOZ5
+erf.dryscal_vert_adv_type    = WENOZ5
+erf.moistscal_horiz_adv_type = WENOZ5
+erf.moistscal_vert_adv_type  = WENOZ5
+
+erf.moisture_model  = "Kessler"
+
+erf.molec_diff_type = "None"
+erf.les_type        = "Smagorinsky"
+erf.Cs              = 0.17
+erf.Pr_t            = 0.333333
+erf.Sc_t            = 0.333333
+
+erf.init_type = "input_sounding"
+erf.init_sounding_ideal = true
+
+erf.add_custom_rhotheta_forcing        = true
+erf.add_custom_moisture_forcing        = true
+erf.add_custom_geostrophic_profile     = true
+erf.add_custom_w_subsidence            = true
+erf.custom_forcing_uses_primitive_vars = false
+
+# Higher values of perturbations lead to instability
+# Instability seems to be coming from BC
+prob.U_0_Pert_Mag = 0.01
+prob.V_0_Pert_Mag = 0.01 
+prob.W_0_Pert_Mag = 0.0
+
+prob.pert_ref_height = 1600.0
+prob.T_0_Pert_Mag    = 0.1
+prob.qv_0_Pert_Mag   = 0.000025
+
+prob.advection_heating_rate   = -2.3148E-5
+prob.source_cutoff            = 1500.0
+prob.source_cutoff_transition = 1500.0
+
+prob.advection_moisture_rate            = -1.2E-8
+prob.moisture_source_cutoff            	= 300.0
+prob.moisture_source_cutoff_transition 	= 200.0
+
+prob.wbar_sub_max    = -0.0065
+prob.wbar_cutoff_max = 1500.0
+prob.wbar_cutoff_min = 2100.0   
+
+prob.custom_TKE      = true

Exec/DevTests/Bomex/input_SAM

@@ -1,13 +1,13 @@
 # ------------------  INPUTS TO MAIN PROGRAM  -------------------
-stop_time = 21600
+stop_time = 43200
 
 amrex.fpe_trap_invalid = 1
 
 fabarray.mfiter_tile_size = 1024 1024 1024
 
 # PROBLEM SIZE & GEOMETRY
-geometry.prob_extent =  6400     6400    4000
-amr.n_cell           =    64       64     100
+geometry.prob_extent =  3200     3200    4000
+amr.n_cell           =    32       32     100
 
 geometry.is_periodic = 1 1 0
 
@@ -17,20 +17,22 @@ erf.most.flux_type = "custom"
 erf.most.ustar  = 0.28   # ustar
 erf.most.tstar  = 8.0e-3 # theta flux
 erf.most.qstar  = 5.2e-5 # qv    flux
-erf.most.z0   = 0.1
+erf.most.z0     = 0.1
 erf.most.zref   = 20.0
 
+// NOTE: This should have a qv grad too (use hoextrapcc?!)
 zhi.type = "SlipWall"
-
+zhi.theta_grad = 0.00365
+
 # TIME STEP CONTROL
-erf.fixed_dt       = 1.0 # fixed time step depending on grid resolution
+erf.fixed_dt       = 0.5 # fixed time step depending on grid resolution
 
 # DIAGNOSTICS & VERBOSITY
 erf.sum_interval   = 1       # timesteps between computing mass
 erf.v              = 1       # verbosity in ERF.cpp
 amr.v              = 1       # verbosity in Amr.cpp
 erf.data_log       = "surf" "mean" "flux" "subgrid"
-erf.profile_int    = 60 
+erf.profile_int    = 120 
 
 # REFINEMENT / REGRIDDING
 amr.max_level       = 0       # maximum level number allowed
@@ -41,12 +43,12 @@ erf.check_int       = 600        # number of timesteps between checkpoints
 
 # PLOTFILES
 erf.plot_file_1     = plt       # prefix of plotfile name
-erf.plot_int_1      = 60        # number of timesteps between plotfiles
+erf.plot_int_1      = 120        # number of timesteps between plotfiles
 erf.plot_vars_1     = density rhotheta x_velocity y_velocity z_velocity pressure temp theta qt qp qv qc qi
 
 # SOLVER CHOICE
 erf.alpha_T = 0.0
-erf.alpha_C = 1.0
+erf.alpha_C = 0.0
 erf.use_gravity = true
 
 erf.dycore_horiz_adv_type    = Upwind_5th
@@ -60,15 +62,17 @@ erf.moisture_model  = "SAM"
 
 erf.molec_diff_type = "None"
 erf.les_type        = "Smagorinsky"
-erf.Cs              = 0.1
+erf.Cs              = 0.17
+erf.Pr_t            = 0.333333
+erf.Sc_t            = 0.333333
 
 erf.init_type = "input_sounding"
 erf.init_sounding_ideal = true
 
-erf.add_custom_rhotheta_forcing = true
-erf.add_custom_moisture_forcing = true
-erf.add_custom_geostrophic_profile = true
-erf.add_custom_w_subsidence     = true
+erf.add_custom_rhotheta_forcing        = true
+erf.add_custom_moisture_forcing        = true
+erf.add_custom_geostrophic_profile     = true
+erf.add_custom_w_subsidence            = true
 erf.custom_forcing_uses_primitive_vars = false
 
 # Higher values of perturbations lead to instability