nichollsh · nichollsh · Jul 19, 2024 · Jul 19, 2024 · Jul 19, 2024 · Jul 19, 2024
diff --git a/CITATION.cff b/CITATION.cff
@@ -5,7 +5,7 @@ authors:
   given-names: "Harrison"
   orcid: "https://orcid.org/0000-0002-8368-4641"
 title: "AGNI"
-version: 0.6.0
+version: 0.6.1
 doi: 10.xx/xx.xx
-date-released: 2024-07-17
+date-released: 2024-07-18
 url: "https://github.com/nichollsh/AGNI"
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "AGNI"
 uuid = "ede838c1-9ec3-4ebe-8ae8-da4091b3f21c"
 authors = ["Harrison Nicholls <[email protected]>"]
-version = "0.6.0"
+version = "0.6.1"
 
 [deps]
 ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"

diff --git a/get_data.sh b/get_data.sh
@@ -2,6 +2,9 @@
 # Download and unpack required and/or optional data
 # All files can be found on OSF at https://osf.io/8dumn/
 
+# Exit script if any of the commands fail
+set -e 
+
 # Check that curl is installed 
 if ! [ -x "$(command -v curl)" ]; then
   echo 'ERROR: curl is not installed.' >&2
@@ -47,64 +50,77 @@ function osf {
 
     # target file path
     tgt="$2/$3"
-    rm -f $tgt
-    echo "    $1 > $tgt"
+
+    # exists?
+    if [[ -f "$tgt" ]]; then
+        echo "    $1 > file already exists"
+        return 0
+    fi
 
     # get data
+    echo "    $1 > $tgt"
     mkdir -p $2
     curl -LsS "https://osf.io/download/$1/" > $tgt
-}
-
-# Handle user input 
-case $1 in
-    "basic")
-        echo $help_basic
-
-        osf qmp4e $res/spectral_files/Oak/318/ Oak.sf
-        osf 5fxr7 $res/spectral_files/Oak/318/ Oak.sf_k
-
-        osf heuza $res/spectral_files/Dayspring/48/ Dayspring.sf
-        osf c5jv3 $res/spectral_files/Dayspring/48/ Dayspring.sf_k
-
-        osf b5gsh $res/spectral_files/Dayspring/256/ Dayspring.sf
-        osf dn6wh $res/spectral_files/Dayspring/256/ Dayspring.sf_k
 
-        osf 2qdu8 $res/stellar_spectra sun.txt
-        ;;
-
-    "highres")
-        echo $help_highres
-
-        osf p672d $res/spectral_files/Honeyside/4096/ Honeyside.sf
-        osf ujb4z $res/spectral_files/Honeyside/4096/ Honeyside.sf_k
-        ;;
-
-    "steam")
-        echo $help_steam
-
-        osf 6rvfe $res/spectral_files/Frostflow/16/ Frostflow.sf
-        osf kxve8 $res/spectral_files/Frostflow/16/ Frostflow.sf_k
-
-        osf 9n6mw $res/spectral_files/Frostflow/48/ Frostflow.sf
-        osf xfap8 $res/spectral_files/Frostflow/48/ Frostflow.sf_k
-
-        osf mnvyq $res/spectral_files/Frostflow/256/ Frostflow.sf
-        osf tzsgc $res/spectral_files/Frostflow/256/ Frostflow.sf_k
-        ;;
+    return 0
+}
 
-    "stellar")
-        echo $help_stellar 
-        osf mabp2 $res/stellar_spectra trappist-1.txt
-        osf rk7mj $res/stellar_spectra eps-eri.txt
-        osf agsrq $res/stellar_spectra hd97658.txt
-        osf ehfsy $res/stellar_spectra gj1214.txt
-        ;;
+# Handle request for downloading a group of data 
+function handle_request {
+    case $1 in
+        "basic")
+            echo $help_basic
+
+            osf qmp4e $res/spectral_files/Oak/318/ Oak.sf
+            osf 5fxr7 $res/spectral_files/Oak/318/ Oak.sf_k
+
+            osf heuza $res/spectral_files/Dayspring/48/ Dayspring.sf
+            osf c5jv3 $res/spectral_files/Dayspring/48/ Dayspring.sf_k
+
+            osf b5gsh $res/spectral_files/Dayspring/256/ Dayspring.sf
+            osf dn6wh $res/spectral_files/Dayspring/256/ Dayspring.sf_k
+
+            osf 2qdu8 $res/stellar_spectra sun.txt
+            ;;
+
+        "highres")
+            echo $help_highres
+
+            osf p672d $res/spectral_files/Honeyside/4096/ Honeyside.sf
+            osf ujb4z $res/spectral_files/Honeyside/4096/ Honeyside.sf_k
+            ;;
+
+        "steam")
+            echo $help_steam
+
+            osf 6rvfe $res/spectral_files/Frostflow/16/ Frostflow.sf
+            osf kxve8 $res/spectral_files/Frostflow/16/ Frostflow.sf_k
+
+            osf 9n6mw $res/spectral_files/Frostflow/48/ Frostflow.sf
+            osf xfap8 $res/spectral_files/Frostflow/48/ Frostflow.sf_k
+
+            osf mnvyq $res/spectral_files/Frostflow/256/ Frostflow.sf
+            osf tzsgc $res/spectral_files/Frostflow/256/ Frostflow.sf_k
+            ;;
+
+        "stellar")
+            echo $help_stellar 
+            osf mabp2 $res/stellar_spectra trappist-1.txt
+            osf rk7mj $res/stellar_spectra eps-eri.txt
+            osf agsrq $res/stellar_spectra hd97658.txt
+            osf ehfsy $res/stellar_spectra gj1214.txt
+            osf 2qdu8 $res/stellar_spectra sun.txt
+            ;;
+
+        *)
+            echo "$help"
+            return 0
+            ;;
+    esac
+    return 0
+}
 
-    *)
-        echo "$help"
-        exit 1
-        ;;
-esac
+handle_request $1
 
 echo "Done!"
 

diff --git a/res/config/55cnce_chem.toml b/res/config/55cnce_chem.toml
@@ -40,12 +40,13 @@ title = "Roughly 55 Cancri e @ fO2=IW"
     thermo_funct    = true               
     sensible_heat   = false               
     latent_heat     = true               
-    convection_type = "mlt"              
+    convection      = true     
     solution_type   = 3                  
     solvers         = ["newton"]         
     dx_max          = 400.0              
     initial_state   = ["iso", "2700"]     
-    linesearch      = false              
+    linesearch      = false     
+    easy_start      = false         
     converge_atol   = 1.0e-2             
     converge_rtol   = 1.0e-3             
 

diff --git a/res/config/condense.toml b/res/config/condense.toml
@@ -36,7 +36,7 @@ title = "Condensation test"
     verbosity       = 1
     max_steps       = 300              
     max_runtime     = 400              
-    num_levels      = 38               
+    num_levels      = 35               
     continua        = true             
     rayleigh        = false            
     cloud           = false            
@@ -45,12 +45,13 @@ title = "Condensation test"
     thermo_funct    = true             
     sensible_heat   = true             
     latent_heat     = true             
-    convection_type = "mlt"            
+    convection      = true  
     solution_type   = 3                
     solvers         = ["newton"]       
     dx_max          = 500.0            
     initial_state   = ["loglin","600"]   
-    linesearch      = true             
+    linesearch      = true  
+    easy_start      = true            
     converge_atol   = 0.1              
     converge_rtol   = 1.0e-3           
 

diff --git a/res/config/default.toml b/res/config/default.toml
@@ -49,12 +49,13 @@ title = "Default"                       # Name for this configuration file
     thermo_funct    = false                     # Use temperature-dependent thermodynamic properties?
     sensible_heat   = false                     # Include sensible heat transport at the surface?
     latent_heat     = false                     # Include heat release from phase change
-    convection_type = ""                        # Convection type (mlt = use mixing length theory).
+    convection      = true                      # Include heat transport by convection
     solution_type   = 0                         # Solution type (see wiki).
     solvers         = []                        # Ordered list of solvers to apply (see wiki).
     dx_max          = 200.0                     # Maximum step size [Kelvin], when using nonlinear solvers
     initial_state   = ["dry", "sat", "H2O"]     # Ordered list of requests describing the initial state of the atmosphere (see wiki).
     linesearch      = false                     # Use linesearch?
+    easy_start      = false                     # Initially down-scale convective/condensation fluxes, if initial guess is poor.   
     converge_atol   = 1.0e-3                    # Convergence criterion on absolute flux divergence [W m-2].
     converge_rtol   = 1.0e-1                    # Convergence criterion on relative flux divergence [dimensionless].
 

diff --git a/res/config/hotdry.toml b/res/config/hotdry.toml
@@ -44,12 +44,13 @@ title = "Hot and dry"
     thermo_funct    = true           
     sensible_heat   = true           
     latent_heat     = false
-    convection_type = "mlt"          
+    convection      = true         
     solution_type   = 3              
     solvers         = ["newton"]     
     dx_max          = 400.0          
     initial_state   = ["iso","2300"] 
-    linesearch      = false          
+    linesearch      = false   
+    easy_start      = false       
     converge_atol   = 1.0e-2         
     converge_rtol   = 1.0e-4         
 

diff --git a/src/AGNI.jl b/src/AGNI.jl
@@ -286,14 +286,15 @@ module AGNI
         flag_aer::Bool         =        cfg["execution" ]["aerosol"]
         overlap::Int           =        cfg["execution" ]["overlap_method"]
         thermo_funct::Bool     =        cfg["execution" ]["thermo_funct"]
-        conv_type::String      =        cfg["execution" ]["convection_type"]
+        incl_convect::Bool     =        cfg["execution" ]["convection"]
         incl_sens::Bool        =        cfg["execution" ]["sensible_heat"]
         incl_latent::Bool      =        cfg["execution" ]["latent_heat"]
         sol_type::Int          =        cfg["execution" ]["solution_type"]
         solvers_cmd::Array{String,1} =  cfg["execution" ]["solvers"]
         initial_req::Array{String,1} =  cfg["execution" ]["initial_state"]
         dx_max::Float64        =        cfg["execution" ]["dx_max"]
         linesearch::Bool       =        cfg["execution" ]["linesearch"]
+        easy_start::Bool       =        cfg["execution" ]["easy_start"]
         conv_atol::Float64     =        cfg["execution" ]["converge_atol"]
         conv_rtol::Float64     =        cfg["execution" ]["converge_rtol"]
         max_steps::Int         =        cfg["execution" ]["max_steps"]
@@ -455,8 +456,6 @@ module AGNI
         end 
 
         # Solver variables 
-        incl_convect::Bool= !isempty(conv_type)
-        use_mlt::Bool     = (conv_type == "mlt")
         modplot::Int      = 0
         incl_conduct::Bool = false
 
@@ -498,9 +497,10 @@ module AGNI
                                     convect=incl_convect, latent=incl_latent,
                                     sens_heat=incl_sens, max_steps=max_steps,
                                     max_runtime=max_runtime, 
-                                    conv_atol=conv_atol,
-                                    conv_rtol=conv_rtol, method=method_idx, 
+                                    conv_atol=conv_atol, conv_rtol=conv_rtol, 
+                                    method=method_idx, 
                                     dx_max=dx_max, linesearch=linesearch,
+                                    easy_start=easy_start,
                                     modplot=modplot,save_frames=plt_ani)
                 return_success = return_success && solver_success
 
@@ -529,7 +529,7 @@ module AGNI
         plt_vmr && plotting.plot_vmr(atmos,      joinpath(atmos.OUT_DIR,"plot_vmrs.png"), size_x=600)
         plt_cff && plotting.plot_contfunc(atmos, joinpath(atmos.OUT_DIR,"plot_contfunc.png"))
         plt_tmp && plotting.plot_pt(atmos,       joinpath(atmos.OUT_DIR,"plot_ptprofile.png"), incl_magma=(sol_type==2))
-        plt_flx && plotting.plot_fluxes(atmos,   joinpath(atmos.OUT_DIR,"plot_fluxes.png"), incl_mlt=use_mlt, incl_eff=(sol_type==3), incl_cdct=incl_conduct, incl_latent=incl_latent)
+        plt_flx && plotting.plot_fluxes(atmos,   joinpath(atmos.OUT_DIR,"plot_fluxes.png"), incl_mlt=incl_convect, incl_eff=(sol_type==3), incl_cdct=incl_conduct, incl_latent=incl_latent)
         plt_ems && plotting.plot_emission(atmos, joinpath(atmos.OUT_DIR,"plot_emission.png"))
         plt_alb && plotting.plot_albedo(atmos,   joinpath(atmos.OUT_DIR,"plot_albedo.png"))
 

diff --git a/src/atmosphere.jl b/src/atmosphere.jl
@@ -169,7 +169,11 @@ module atmosphere
         # Conduction 
         flux_cdct::Array{Float64,1}         # Conductive flux [W m-2]
 
-        # Phase change 
+        # Phase change
+        phs_tau_mix::Float64                # Time scale (mixed composition)
+        phs_tau_sgl::Float64                # Time scale (single gas)
+        phs_wrk_df::Array{Float64,1}        # work array: flux difference
+        phs_wrk_fl::Array{Float64,1}        # work array: edge fluxes
         flux_l::Array{Float64, 1}           # Latent heat energy flux [W m-2]
         mask_l::Array{Bool,1}               # Layers transporting latent heat
 
@@ -310,7 +314,7 @@ module atmosphere
         end
 
         # Code versions 
-        atmos.AGNI_VERSION = "0.6.0"
+        atmos.AGNI_VERSION = "0.6.1"
         atmos.SOCRATES_VERSION = readchomp(joinpath(ENV["RAD_DIR"],"version"))
         @debug "AGNI VERSION = $(atmos.AGNI_VERSION)"
         @debug "Using SOCRATES at $(ENV["RAD_DIR"])"
@@ -416,6 +420,10 @@ module atmosphere
         atmos.cloud_arr_l   = zeros(Float64, atmos.nlev_c)
         atmos.cloud_arr_f   = zeros(Float64, atmos.nlev_c) 
 
+        # Phase change timescales [seconds]
+        atmos.phs_tau_mix = 1.0e4   # mixed composition case
+        atmos.phs_tau_sgl = 1.0e4   # single gas case
+
         # Hardcoded cloud properties 
         atmos.cond_alpha    = 0.0     # 0% of condensate is retained (i.e. complete rainout)
         atmos.cloud_val_r   = 1.0e-5  # 10 micron droplets
@@ -1347,10 +1355,12 @@ module atmosphere
         atmos.mask_l =            falses(atmos.nlev_l)      # Phase change 
         atmos.mask_c =            falses(atmos.nlev_l)      # Dry convection
 
+        atmos.phs_wrk_df =        zeros(Float64, atmos.nlev_c)  # flux difference
+        atmos.phs_wrk_fl =        zeros(Float64, atmos.nlev_l)  # edge fluxes
         atmos.flux_l =            zeros(Float64, atmos.nlev_l)  # Latent heat / phase change 
         atmos.flux_cdry =         zeros(Float64, atmos.nlev_l)  # Dry convection 
         atmos.flux_cdct =         zeros(Float64, atmos.nlev_l)  # Conduction 
-        atmos.Kzz =               zeros(Float64, atmos.nlev_l)
+        atmos.Kzz =               zeros(Float64, atmos.nlev_l)  # eddy diffusion coeff.
 
         atmos.flux_tot =          zeros(Float64, atmos.nlev_l)
         atmos.flux_dif =          zeros(Float64, atmos.nlev_c)

diff --git a/src/dump.jl b/src/dump.jl
@@ -85,8 +85,8 @@ module dump
         # into PROTEUS without compatibility issues.
 
         # Absorb output from these calls, because they spam the Debug logger
-        @debug "ALL OUTPUT SUPPRESSED"
-        with_logger(NullLogger()) do
+        @debug "ALL DEBUG SUPPRESSED"
+        with_logger(MinLevelLogger(current_logger(), Logging.Info-200)) do
 
             ds = Dataset(fname,"c")
 
@@ -327,8 +327,9 @@ module dump
             var_albs[:] = atmos.albedo_s_arr
 
             close(ds)
+
         end # suppress output 
-        @debug "ALL OUTPUT RESTORED"
+        @debug "ALL DEBUG RESTORED"
 
         return nothing
     end # end write_ncdf