Merge pull request #54 from nichollsh/chemfix

Fixes to chemistry following thermo changes

CITATION.cff

@@ -5,7 +5,7 @@ authors:
   given-names: "Harrison"
   orcid: "https://orcid.org/0000-0002-8368-4641"
 title: "AGNI"
-version: 0.5.1
+version: 0.5.2
 doi: 10.xx/xx.xx
 date-released: 2024-06-25
 url: "https://github.com/nichollsh/AGNI"

Project.toml

@@ -1,7 +1,7 @@
 name = "AGNI"
 uuid = "ede838c1-9ec3-4ebe-8ae8-da4091b3f21c"
 authors = ["Harrison Nicholls <[email protected]>"]
-version = "0.5.1"
+version = "0.5.2"
 
 [deps]
 ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"

res/config/chemistry.toml

@@ -2,58 +2,58 @@
 title = "Equilibrium chemistry demo"                    # Name for this configuration file
 
 [planet]
-    tmp_surf        = 2200.0            # Surface temperature [kelvin]
-    instellation    = 44000.0          # Stellar flux at planet's orbital distance [W m-2]
-    albedo_b        = 0.18              # Pseudo bond-albedo which downscales the stellar flux by 1-this_value
-    s0_fact         = 0.375             # Stellar flux scale factor which accounts for planetary rotation (c.f. Cronin+13)
-    zenith_angle    = 48.19             # Characteristic zenith angle for incoming stellar radiation [degrees]
-    albedo_s        = 0.0               # Surface albedo
-    radius          = 6.37e6            # Planet radius at the surface [m]
-    gravity         = 9.81              # Gravitational acceleration at the surface [m s-2]
-    p_surf          = 270.0             # Total surface pressure [bar]
-    p_top           = 1e-5              # Total top-of-atmosphere pressure [bar]
-    vmr             = { H2O = 0.6, CO2=0.1, N2=0.1, SO2=0.1, O2=0.05, Fe=0.05}     # Volatile volume mixing ratios
+    tmp_surf        = 2200.0    
+    instellation    = 10000.0   
+    albedo_b        = 0.0      
+    s0_fact         = 0.375     
+    zenith_angle    = 48.19     
+    albedo_s        = 0.0       
+    radius          = 6.37e6    
+    gravity         = 9.81      
+    p_surf          = 270.0     
+    p_top           = 1e-5      
+    vmr             = { H2O = 0.3, CO2=0.1, N2=0.1, SO2=0.05, O2=0.05, FeO2=0.05, OH=0.0, H=0.0, CH4=0.1, CO=0.5, H2=0.5, SO=0.0, NH3=0.0, NH2=0.0, H2S=0.0, H2SO4=0.0}     # Volatile volume mixing ratios
     condensates     = []
-    tmp_int         = 0.0               # Effective temperature
-
+    tmp_int         = 0.0    
+    
 [files]
     clean_output    = true
-    input_sf        = "res/spectral_files/Dayspring/48/Dayspring.sf"    # Path to SOCRATES spectral file.
+    input_sf        = "res/spectral_files/nogit/Dayspring/48/Dayspring.sf"    # Path to SOCRATES spectral file.
     input_star      = "res/stellar_spectra/sun.txt"                     # Path to stellar spectrum.
     output_dir      = "out/"                                            # Path to output directory.
     fastchem_path   = "/Users/nichollsh/Projects/fastchem/"
 
 [execution]
-    verbosity       = 1                         # Log level (0: none, 1: normal, 2: debug)
-    max_steps       = 200                       # Maximum number of solver steps.
-    max_runtime     = 400                       # Maximum wall-clock solver runtime [s].
-    num_levels      = 40                        # Number of model levels.
-    continua        = true                      # Include absorption from continua?
-    rayleigh        = false                      # Include rayleigh scattering?
-    cloud           = false                     # Include water cloud radiative properties?
-    aerosol         = false                     # Include aerosol radiative properties?
-    overlap_method  = 4                         # Method for treating line overlap.
-    thermo_funct    = false                     # Use temperature-dependent thermodynamic properties?
-    sensible_heat   = false                     # Include sensible heat transport at the surface?
-    latent_heat     = false                     
-    convection_type = "mlt"                     # Convection type ("" = no convection, "mlt" = use mixing length theory).
-    chemistry       = 1                         # Chemistry type (see wiki)
-    solution_type   = 3                         # Solution type (see wiki).
-    solvers         = ["newton"]                # Ordered list of solvers to apply (see wiki).
-    dx_max          = 200.0                     # Maximum step size [Kelvin], when using nonlinear solvers
-    initial_state   = ["iso","2000"]            # Ordered list of requests describing the initial state of the atmosphere (see wiki).
-    linesearch      = false                     # Use linesearch?
-    converge_atol   = 1.0e-2                    # Convergence criterion on absolute flux lost [W m-2].
-    converge_rtol   = 1.0e-4                    # Convergence criterion on relative flux lost [dimensionless].
+    verbosity       = 1                        
+    max_steps       = 200                      
+    max_runtime     = 400                      
+    num_levels      = 45                       
+    continua        = true                     
+    rayleigh        = true                    
+    cloud           = false                    
+    aerosol         = false                    
+    overlap_method  = 4                        
+    thermo_funct    = true                    
+    sensible_heat   = false                    
+    latent_heat     = false                    
+    convection_type = "mlt"                    
+    chemistry       = 1                        
+    solution_type   = 3                        
+    solvers         = ["newton"]               
+    dx_max          = 200.0                    
+    initial_state   = ["iso","2000"]           
+    linesearch      = false                    
+    converge_atol   = 1.0e-2                   
+    converge_rtol   = 1.0e-4                   
 
 
 [plots]
-    at_runtime      = true                      # Make some plots at runtime?
-    temperature     = true                      # Plot temperature profile?
-    fluxes          = true                      # Plot fluxes?
-    contribution    = true                      # Plot spectral contribution function?
-    emission        = true                      # Plot emission spectrum?
-    albedo          = true                      # Plot spectral albedo?
-    mixing_ratios   = true                      # Plot mixing ratios?
-    animate         = true                     # Make animation from runtime plots?
+    at_runtime      = true                
+    temperature     = true                
+    fluxes          = true                
+    contribution    = true                
+    emission        = true                
+    albedo          = true                
+    mixing_ratios   = true                
+    animate         = true                
 

src/atmosphere.jl

@@ -110,8 +110,9 @@ module atmosphere
         gas_sat::Dict{String, Array{Bool, 1}}       # Layer is saturated or cold-trapped
         gas_dat::Dict{String, phys.Gas_t}           # struct variables containing thermodynamic data
         gas_yield::Dict{String, Array{Float64,1}}   # condensate yield [kg/m^2] at each level (can be negative, representing evaporation)
-        condensates::Array{String, 1}                   # List of condensing gases (strings)
-        single_component::Bool                          # Does a single gas make up 100% of layer at any point in the column?
+        condensates::Array{String, 1}               # List of condensing gases (strings)
+        condense_any::Bool                          # length(condensates)>0 ?
+        single_component::Bool                      # Does a single gas make up 100% of layer at any point in the column?
 
         # Gases (only those in spectralfile)
         gas_soc_num::Int 
@@ -301,7 +302,7 @@ module atmosphere
         end
 
         # Code versions 
-        atmos.AGNI_VERSION = "0.5.1"
+        atmos.AGNI_VERSION = "0.5.2"
         atmos.SOCRATES_VERSION = readchomp(joinpath(ENV["RAD_DIR"],"version"))
         @debug "AGNI VERSION = $(atmos.AGNI_VERSION)"
         @debug "Using SOCRATES at $(ENV["RAD_DIR"])"
@@ -523,7 +524,9 @@ module atmosphere
         end 
 
         # Validate condensate names 
+        atmos.condense_any = false
         if length(condensates) > 0
+            atmos.condense_any = true
             for c in condensates
                 if !(c in atmos.gas_names)
                     @error "Invalid condensate '$c'"
@@ -1081,7 +1084,7 @@ module atmosphere
             if !isempty(gas_flags)
                 gas_flags = "($(gas_flags[1:end-1]))"
             end 
-            @info @sprintf("    %6.2e %-5s %s", atmos.gas_vmr[g][end], g, gas_flags)
+            @info @sprintf("    %6.2e %-6s %s", atmos.gas_vmr[g][end], g, gas_flags)
         end 
 
 
@@ -1211,12 +1214,14 @@ module atmosphere
     - `atmos::Atmos_t`                  the atmosphere struct instance to be used.
     - `chem_type::Int`                  chemistry type (see wiki)
     - `write_cfg::Bool`                 write config and elements
-    - `tmp_floor::Float64=500.0`        temperature floor for T(p) provided to FastChem
+    - `tmp_floor::Float64`              temperature floor for T(p) provided to FastChem
 
     Returns:
     - `state::Int`                      fastchem state (0: success, 1: critical_fail, 2: elem_fail, 3: conv_fail, 4: both_fail)
     """
-    function chemistry_eq!(atmos::atmosphere.Atmos_t, chem_type::Int, write_cfg::Bool; tmp_floor::Float64=500.0)::Int
+    function chemistry_eq!(atmos::atmosphere.Atmos_t, chem_type::Int, write_cfg::Bool; tmp_floor::Float64=700.0)::Int
+
+        @debug "Running equilibrium chemistry"
 
         # Return code 
         state::Int = 0
@@ -1227,6 +1232,14 @@ module atmosphere
             return 1
         end 
 
+        # Check minimum temperature 
+        if maximum(atmos.tmpl) < tmp_floor 
+            @warn "Temperature profile is entirely too cold for FastChem. Not doing chemistry."
+            return 1
+        end 
+
+        count_elem_nonzero::Int = 0
+
         # Paths
         execpath::String = joinpath(atmos.fastchem_path,"fastchem")             # Executable file 
         confpath::String = joinpath(atmos.fastchem_work,"config.input")         # Configuration by AGNI
@@ -1263,16 +1276,16 @@ module atmosphere
                 write(f,joinpath(logK,"logK.dat")*" "*joinpath(logK,"logK_condensates.dat")*" \n\n")
 
                 write(f,"#Accuracy of chemistry iteration \n")
-                write(f,"1.0e-5 \n\n")
+                write(f,"1.0e-4 \n\n")
 
                 write(f,"#Accuracy of element conservation \n")
                 write(f,"1.0e-4 \n\n")
 
                 write(f,"#Max number of chemistry iterations  \n")
-                write(f,"50000 \n\n")
+                write(f,"60000 \n\n")
 
                 write(f,"#Max number internal solver iterations  \n")
-                write(f,"10000 \n\n")
+                write(f,"30000 \n\n")
             end
 
             # Calculate elemental abundances 
@@ -1289,16 +1302,19 @@ module atmosphere
                         N_g[i] += d[e]
                     end 
                 end 
+                # will be normalised in later code 
                 N_g *= get_x(atmos, gas, atmos.nlev_c) * atmos.p[end] / (phys.k_B * atmos.tmp[end])  # gas contribution
-                N_t += N_g  # number/m^3
+                N_t += N_g  
             end 
 
             # Write elemental abundances 
             open(joinpath(atmos.fastchem_work,"elements.dat"),"w") do f
                 write(f,"# Elemental abundances derived from AGNI volatiles \n")
                 for (i,e) in enumerate(phys.elements_list)
                     if N_t[i] > 1.0e-30
+                        # normalise relative to hydrogen
                         write(f, @sprintf("%s    %.3f \n",e,log10(N_t[i]/N_t[1]) + 12.0))
+                        count_elem_nonzero += 1
                     end
                 end 
             end 
@@ -1309,7 +1325,7 @@ module atmosphere
             write(f,"# AGNI temperature structure \n")
             write(f,"# bar, kelvin \n")
             for i in 1:atmos.nlev_c 
-                write(f,@sprintf("%.6e    %.6e \n", atmos.p[i], max(tmp_floor,atmos.tmp[i]) ))
+                write(f,@sprintf("%.6e    %.6e \n", atmos.p[i]*1e-5, max(tmp_floor,atmos.tmp[i]) ))
             end 
         end 
 
@@ -1350,24 +1366,77 @@ module atmosphere
         (data,head) = readdlm(chempath, '\t', Float64, header=true)
         data = transpose(data)  # convert to: gas, level
 
+        # Clear VMRs 
+        for g in atmos.gas_names
+            fill!(atmos.gas_vmr[g], 0.0)
+        end 
+
         # Parse gas chemistry
-        g::String = ""
+        g_fc::String = "_unset"
+        d_fc::Dict = Dict{String, Int}()
+        g_in::String = "_unset"
+        match::Bool = false 
         N_t = data[4,:] # at each level: sum of gas number densities 
+
         for (i,h) in enumerate(head)  # for each column (gas)
-            g = rstrip(lstrip(h))
-
-            # check if gas is included in the model
-            if g in keys(phys.map_fastchem_name) 
-                g = phys.map_fastchem_name[g]  # convert name
-                if g in atmos.gas_names
-                    N_g = data[i,:]  # number densities for this gas 
-                    atmos.gas_vmr[g][:] .= N_g[:] ./ N_t[:]    # mole fraction (VMR) for this gas 
-                end
-            end # not included => skip
+
+            # skip T and P 
+            if i <= 5+count_elem_nonzero
+                continue 
+            end 
+
+            # parse name 
+            g_fc = rstrip(lstrip(h))
+            if occursin("_", g_fc)
+                g_fc = split(g_fc, "_")[1]
+            end
+            g_fc = replace(g_fc, "cis"=>"", "trans"=>"")
+
+            match = false
+
+            # firstly, check if we have the FC name already stored
+            for g in atmos.gas_names
+                if atmos.gas_dat[g].fastchem_name == g_fc 
+                    match = true 
+                    g_in = g
+                    break
+                end 
+            end 
+
+            # not stored => search based on atoms 
+            if !match 
+                d_fc = phys.count_atoms(g_fc)  # get atoms dict from FC name 
+
+                for g in atmos.gas_names
+                    if phys.same_atoms(d_fc, atmos.gas_dat[g].atoms)
+                        match = true
+                        g_in = g
+                        break 
+                    end
+                end 
+            end 
+
+            # matched?
+            if match 
+                N_g = data[i,:]  # number densities for this gas 
+                atmos.gas_vmr[g_in][:] .+= N_g[:] ./ N_t[:]    # mole fraction (VMR) for this gas 
+            end 
         end 
 
-        # Do not renormalise mixing ratios
+        # Do not renormalise mixing ratios, since this is done by fastchem
+        # If we are missing gases then that's okay.
+
+        # Find where we truncated the temperature profile, and make sure that regions above that use the same x_gas values 
+        for i in range(start=atmos.nlev_c, stop=1, step=-1)
+            if atmos.tmp[i] < tmp_floor
+                for g in atmos.gas_names 
+                    atmos.gas_vmr[g][1:i] .= atmos.gas_vmr[g][i+1]
+                end 
+                break 
+            end 
+        end 
 
+        # See docstring for return codes
         return state 
     end
 

src/energy.jl

@@ -459,7 +459,7 @@ module energy
     function condense_relax!(atmos::atmosphere.Atmos_t)
 
         # Check if empty
-        if length(atmos.condensates) == 0
+        if !atmos.condense_any
             return nothing 
         end 
 
@@ -542,7 +542,7 @@ module energy
         fill!(atmos.mask_l, 0)
 
         # Check if empty
-        if length(atmos.condensates) == 0
+        if !atmos.condense_any
             return nothing 
         end 
 
@@ -600,7 +600,7 @@ module energy
         fill!(atmos.flux_dif, 0.0)
 
         # +Condensation energy flux
-        if latent
+        if latent || atmos.condense_any
             if atmos.single_component
                 # does NOT modify VMRs
                 energy.condense_relax!(atmos)