Merge pull request #55 from nichollsh/chem_storage

Updated syntax for composition stuff

CITATION.cff

@@ -5,7 +5,7 @@ authors:
   given-names: "Harrison"
   orcid: "https://orcid.org/0000-0002-8368-4641"
 title: "AGNI"
-version: 0.5.2
+version: 0.5.3
 doi: 10.xx/xx.xx
-date-released: 2024-06-25
+date-released: 2024-07-02
 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 = "0.5.2"
+version = "0.5.3"
 
 [deps]
 ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"

docs/src/usage.md

@@ -25,24 +25,25 @@ but the model will return an error naming any parameters which are both
 necessary and absent.
 
 Broadly, the configuration files are broken up into four sections:
-* `[planet]` describes general characteristics of the planet and its atmosphere
-* `[files]` lists input/output files
-* `[execution]` describes what the model should do
-* `[plots]` describes which kind of plot to produce
+* `[planet]` -  general characteristics of the planet
+* `[files]` - input/output files and other paths
+* `[composition]` - atmospheric composition and chemistry
+* `[execution]` - what the model should do
+* `[plots]` - which plots should be produced
 
-Some `execution` parameters:
-* `solution_type` tells the model which state to solve for. The allowed values (integers) are...
+Some parameters:
+* `execution.solution_type` tells the model which state to solve for. The allowed values (integers) are...
      - 1 : zero flux divergence at fixed `tmp_surf`
      - 2 : zero flux divergence, with `tmp_surf` set such that the conductive skin (CBL) conserves energy flux
      - 3 : the net upward flux at each layer is equal to `flux_int = sigma * tmp_int^4`
 
-* `solvers` tells the model which solvers to use. This is a list of strings, so multiple solvers can be applied sequentially. An empty string is always appended to the end of this list. Allowed solvers are...
+* `execution.solvers` tells the model which solvers to use. This is a list of strings, so multiple solvers can be applied sequentially. An empty string is always appended to the end of this list. Allowed solvers are...
      - [empty string] : no solving takes place, so the model just calculates fluxes using the initial state
      - `newton` : the Newton-Raphson algorithm is used
      - `gauss`  : the Gauss-Newton algorithm is used 
      - `levenberg` : the Levenberg–Marquardt algorithm is used 
 
-* `initial_state` describes the initial temperature profile applied to the atmosphere. This is a list of strings which are applied in the given order, which allows the user to describe a specific state as required. The descriptors are listed below, some of which take a single argument that needs to immediately follow the descriptor in the list order.
+* `execution.initial_state` describes the initial temperature profile applied to the atmosphere. This is a list of strings which are applied in the given order, which allows the user to describe a specific state as required. The descriptors are listed below, some of which take a single argument that needs to immediately follow the descriptor in the list order.
      - `dry` : integrate the dry adiabatic lapse rate from the surface upwards
      - `str`, `arg` : apply an isothermal stratosphere at `arg` kelvin
      - `iso`, `arg` : set the whole atmosphere to be isothermal at `arg` kelvin
@@ -51,8 +52,8 @@ Some `execution` parameters:
      - `sat` : ensure that no supersaturation occurs at the surface by removing gases as required    
 
     For example, setting `initial_state = ["dry", "sat", "H2O", "str", "180"]` will set T(p) to follow the dry adiabat from the surface, the water condensation curve above that, and then to be isothermal at 180 K until the top of the model.
-   
-* `chem_type` describes the type of chemistry to implement within the model. This is handled externally by FastChem. You must also provide the path to the FastChem installation directory `fastchem_path` in the `[files]` section. The allowed values (integers) are...
+
+* `composition.chem_type` describes the type of chemistry to implement within the model. This is handled externally by FastChem. You must also provide the path to the FastChem installation directory `fastchem_path` in the `[files]` section. The allowed values (integers) are...
      - 0 : Disabled 
      - 1 : Equilibrium, gas phase only
      - 2 : Equilibrium, with condensation (condensates retained)

res/config/55cnce_chem.toml

@@ -10,29 +10,25 @@ title = "Roughly 55 Cancri e @ fO2=IW-4"
     albedo_s        = 0.0            
     radius          = 1.1959e7 
     gravity         = 22.304  
-    p_surf          = 854.894   
-    p_top           = 1e-6           
-
-    # Set surface abundances 
-    # First 6 are set by outgassing code 
-    # SO2, FeO2 set to 0.01 to "sprinkle in" some S and Fe 
-    # Others set to zero but allowed to be modelled
-    vmr             = { H2O=0.0017, CO2=0.0, N2=0.0001, H2=0.5837, CO=0.4095, CH4=0.005,    SO2=0.01, FeO2=0.01,     O2=0.00, OH=0.0, H=0.0, SO=0.0, NH3=0.0, NH2=0.0, H2S=0.0, H2SO4=0.0}    
-    condensates     = []               
     tmp_int         = 0.0
     turb_coeff      = 0.001           
-    wind_speed      = 2.0             
-
+    wind_speed      = 2.0      
+           
 [files]
-    clean_output    = true
     input_sf        = "res/spectral_files/nogit/Dayspring/48/Dayspring.sf"   
     input_star      = "res/stellar_spectra/sun.txt"                       
-    input_vmr       = ""                                                     
     output_dir      = "out/"       
     fastchem_path   = "/Users/nichollsh/Projects/fastchem/"
-
+
+[composition]
+    p_top           = 1e-6     
+    p_dict          = {H2O=1.435, CO2=0.11, N2=0.043, H2=499.004, CO=350.044, CH4=4.258,    SO2=0.01, FeO2=0.01}
+    include_all     = true 
+    chemistry       = 1                  
+    condensates     = []               
 
 [execution]
+    clean_output    = true
     verbosity       = 1                  
     max_steps       = 20000              
     max_runtime     = 400                
@@ -46,8 +42,6 @@ title = "Roughly 55 Cancri e @ fO2=IW-4"
     sensible_heat   = true               
     latent_heat     = true               
     convection_type = "mlt"              
-    condensates     = []                 
-    chemistry       = 1                  
     solution_type   = 3                  
     solvers         = ["newton"]         
     dx_max          = 200.0              

res/config/condense.toml

@@ -1,5 +1,5 @@
 # AGNI configuration file 
-title = "Condensation test"                    # Name for this configuration file
+title = "Condensation test"        
 
 [planet]
     tmp_surf        = 2000.0          
@@ -10,10 +10,6 @@ title = "Condensation test"                    # Name for this configuration fil
     albedo_s        = 0.2             
     radius          = 6.37e6          
     gravity         = 9.81            
-    p_surf          = 7000.0          
-    p_top           = 1e-5            
-    vmr             = { H2O=0.8, CO2=0.1, CH4=0.08, H2=0.02}    
-    condensates     = ["H2O", "CO2"]
     tmp_int         = 0.0            
     turb_coeff      = 1.0e-4
     wind_speed      = 10.0
@@ -27,8 +23,17 @@ title = "Condensation test"                    # Name for this configuration fil
     input_star      = "res/stellar_spectra/sun.txt"                         
     output_dir      = "out/"                                                
 
+[composition]
+    p_surf          = 7000.0          
+    p_top           = 1e-5            
+    vmr_dict        = { H2O=0.8, CO2=0.1, CH4=0.08, H2=0.02}    
+    include_all     = false
+    chemistry       = 0                 
+    condensates     = ["H2O", "CO2"]    
+
 [execution]
-    verbosity       = 1                
+    clean_output    = true             
+    verbosity       = 1
     max_steps       = 300              
     max_runtime     = 200              
     num_levels      = 35               
@@ -41,7 +46,6 @@ title = "Condensation test"                    # Name for this configuration fil
     sensible_heat   = true             
     latent_heat     = true             
     convection_type = "mlt"            
-    chemistry       = 0             
     solution_type   = 1                
     solvers         = ["newton"]       
     dx_max          = 600.0            

res/config/default.toml

@@ -1,20 +1,18 @@
-# AGNI configuration file 
 # This is the default configuration file - it does not solve for RCE
+# The variables are explained below. If you want to model your own conditions, 
+# try making a copy of this file and then modifying it.
+
 title = "Default"                       # Name for this configuration file
 
 [planet]
     tmp_surf        = 2000.0            # 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
+    albedo_b        = 0.18              # Pseudo bond-albedo which downscales the stellar flux by 1-this_value
     s0_fact         = 0.6652            # Stellar flux scale factor which accounts for planetary rotation (c.f. Cronin+13)
     zenith_angle    = 60.0              # 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 = 1.0 }     # Volatile volume mixing ratios
-    condensates     = []                # List of condensable gases
     skin_d          = 0.01              # Conductive skin thickness [m]. Used when sol_type=2.
     skin_k          = 2.0               # Conductive skin conductivity [W m-1 K-1]. Used when sol_type=2.
     tmp_magma       = 3000.0            # Magma temperature [K]. Used when sol_type=2.
@@ -23,13 +21,21 @@ title = "Default"                       # Name for this configuration file
     wind_speed      = 2.0               # Effective wind speed for sensible heat [m s-1].
 
 [files]
-    clean_output    = true
-    input_sf        = "res/spectral_files/Frostflow/256/Frostflow.sf"    # Path to SOCRATES spectral file.
+    input_sf        = "res/spectral_files/Frostflow/256/Frostflow.sf"   # Path to SOCRATES spectral file.
     input_star      = "res/stellar_spectra/sun.txt"                     # Path to stellar spectrum.
-    input_vmr       = ""                                                # Path to input volume mixing ratios. Not required if planet.vmr is passed.
     output_dir      = "out/"                                            # Path to output directory.
 
+[composition]
+    p_surf          = 270.0                     # Total surface pressure [bar]
+    p_top           = 1e-5                      # Total top-of-atmosphere pressure [bar] 
+    vmr_dict        = { H2O = 1.0}              # Volatile volume mixing ratios (=mole fractions)
+    vmr_path        = ""                        # Path to input volume mixing ratios. Not required if planet.vmr is passed.
+    include_all     = false                     # Track extra gases, even when their mixing ratio is zero
+    chemistry       = 0                         # Chemistry type (see wiki)
+    condensates     = []                        # List of volatiles which are allowed to condense.    
+
 [execution]
+    clean_output    = true                      # Clean the output folder at model startup
     verbosity       = 1                         # Log level (0: none, 1: normal, 2: debug)
     max_steps       = 20000                     # Maximum number of solver steps.
     max_runtime     = 400                       # Maximum wall-clock solver runtime [s].
@@ -43,8 +49,6 @@ title = "Default"                       # Name for this configuration file
     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).
-    condensates     = []                        # List of volatiles which are allowed to condense.
-    chemistry       = 0                         # Chemistry type (see wiki
     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