Generalise stellar wrapper, dummy star module

examples/default/init_coupler.toml

@@ -90,7 +90,7 @@ author  = "Harrison Nicholls, Tim Lichtenberg"
     mass    = 1.0       # M_sun
     radius  = 1.0       # R_sun
     Teff    = 5772.0    # K
-    Lbol    = 1.0       # L_sun
+    lum_now = 1.0       # L_sun
     omega   = 50.0      # rotation percentile
     age_now = 4.567     # Gyr, current age of star used for scaling
     age_ini = 0.100     # Gyr, model initialisation/start age

examples/hd63433d/init_coupler.toml

@@ -90,7 +90,7 @@ author  = "Harrison Nicholls, Tim Lichtenberg"
     mass    = 0.99      # M_sun
     radius  = 0.912     # R_sun
     Teff    = 5640.0    # K
-    Lbol    = 0.753     # L_sun
+    lum_now = 0.753     # L_sun
     omega   = 50.0      # rotation percentile
     age_now = 4.140     # Gyr, current age of star used for scaling
     age_ini = 0.100     # Gyr, model initialisation/start age

input/default.toml

@@ -87,15 +87,14 @@ author  = "Harrison Nicholls, Tim Lichtenberg"
 [star]
 
     # Physical parameters
-    mass    = 1.0       # M_sun
     radius  = 1.0       # R_sun
     Teff    = 5772.0    # K
-    Lbol    = 1.0       # L_sun
+    mass    = 1.0       # M_sun
+    lum_now = 1.0       # L_sun, Luminosity as observed today.
     omega   = 50.0      # rotation percentile
     age_now = 4.567     # Gyr, current age of star used for scaling
     age_ini = 0.100     # Gyr, model initialisation/start age
 
-
     module  = "mors"
     [star.mors]
         tracks  = "spada"   # evolution tracks: spada | baraffe

input/dummy.toml

@@ -87,15 +87,14 @@ author  = "Harrison Nicholls, Tim Lichtenberg"
 [star]
 
     # Physical parameters
-    mass    = 1.0       # M_sun
     radius  = 1.0       # R_sun
     Teff    = 5772.0    # K
-    Lbol    = 1.0       # L_sun
+    mass    = 1.0       # M_sun
+    lum_now = 1.0       # L_sun, Luminosity as observed today.
     omega   = 50.0      # rotation percentile
     age_now = 4.567     # Gyr, current age of star used for scaling
     age_ini = 0.100     # Gyr, model initialisation/start age
 
-
     module  = "mors"
     [star.mors]
         tracks  = "baraffe"   # evolution tracks: spada | baraffe

input/dummy_star.toml

@@ -0,0 +1,233 @@
+# PROTEUS configuration file (version 2.0)
+
+# Root tables should be physical, with the exception of "params"
+# Software related options should go within the appropriate physical table
+
+# The general structure is:
+#   [root]     metadata
+#   [params]   parameters for code execution, output files, time-stepping, convergence
+#   [star]     stellar parameters, model selection
+#   [orbit]    planetary orbital parameters
+#   [struct]   planetary structure (mass, radius)
+#   [atmos]    atmosphere parameters, model selection
+#   [escape]   escape parameters, model selection
+#   [interior] magma ocean model selection and parameters
+#   [outgas]   outgassing parameters (fO2) and included volatiles
+#   [delivery] initial volatile inventory, and delivery model selection
+
+# ----------------------------------------------------
+# Metadata
+version = "2.0"
+author  = "Harrison Nicholls, Tim Lichtenberg"
+
+# ----------------------------------------------------
+# Parameters
+[params]
+    # output files
+    [params.out]
+        path        = "dummy_star"
+        logging     = "DEBUG"
+        plot_mod    = 0      # Plotting frequency, 0: wait until completion | n: every n iterations
+        plot_fmt    = "png"  # Plotting image file format, "png" or "pdf" recommended
+
+    # time-stepping
+    [params.dt]
+        minimum      = 1e2    # yr, minimum time-step
+        maximum      = 3e7    # yr, maximum time-step
+        initial      = 1e2    # yr, inital step size
+        starspec     = 1e7    # yr, interval to re-calculate the stellar spectrum
+        starinst     = 1e1    # yr, interval to re-calculate the instellation
+        method       = "adaptive"  # proportional | adaptive | maximum
+
+        [params.dt.proportional]
+            propconst    = 52.0   # Proportionality constant
+
+        [params.dt.adaptive]
+            atol         = 0.02   # Step size atol
+            rtol         = 0.10   # Step size rtol
+
+    # termination criteria
+    [params.stop]
+
+        # required number of iterations
+        [params.stop.iters]
+            enabled = true
+            minimum = 3
+            maximum = 9000
+
+        # required time constraints
+        [params.stop.time]
+            enabled = true
+            minimum = 1.0e3     # yr, model will certainly run to t > minimum
+            maximum = 4.567e+9     # yr, model will terminate when t > maximum
+
+        # solidification
+        [params.stop.solid]
+            enabled  = false
+            phi_crit = 0.005  # non-dim., model will terminate when global melt fraction < phi_crit
+
+        # radiative equilibrium
+        [params.stop.radeqm]
+            enabled = false
+            F_crit  = 0.2     # W m-2, model will terminate when |F_atm| < F_crit
+
+        # steady state
+        [params.stop.steady]
+            enabled  = false
+            F_crit   = 0.8        # Maximum absolute value of F_atm allowed for convergence
+            dprel    = 1.0e-9     # Percentage change in melt fraction over time (dp/p)/dt*100
+
+        [params.stop.escape]
+            enabled   = true
+            mass_frac = 3e-4      # Stop when atm_mass < this frac of initial mass
+
+
+# ----------------------------------------------------
+# Star
+[star]
+
+    # Physical parameters
+    radius  = 1.0       # R_sun
+    Teff    = 5772.0    # K
+    mass    = 1.0       # M_sun
+    lum_now = 1.0       # L_sun, Luminosity as observed today.
+    omega   = 50.0      # rotation percentile
+    age_now = 4.567     # Gyr, current age of star used for scaling
+    age_ini = 0.100     # Gyr, model initialisation/start age
+
+    module  = "dummy"
+    [star.mors]
+        tracks  = "baraffe"   # evolution tracks: spada | baraffe
+        spec    = "stellar_spectra/Named/sun.txt" # stellar spectrum
+
+# Orbital system
+[orbit]
+    semimajoraxis   = 1.0       # AU
+    eccentricity    = 0.0       # dimensionless
+    zenith_angle    = 48.19     # degrees
+    s0_factor       = 0.375     # dimensionless
+
+    # No module specifically for tides / orbital dynamics
+    module  = "none"
+
+
+# Planetary structure - physics table
+[struct]
+    mass        = 1.0       # M_earth
+    radius      = 1.0       # R_earth
+    corefrac    = 0.55      # non-dim., radius fraction
+
+    # No module for specifically for internal structure
+    module  = "none"
+
+# Atmosphere - physics table
+[atmos_clim]
+    prevent_warming = true      # do not allow the planet to heat up
+    surface_d       = 0.01      # m, conductive skin thickness
+    surface_k       = 2.0       # W m-1 K-1, conductive skin thermal conductivity
+    cloud_enabled   = false     # enable water cloud radiative effects
+    cloud_alpha     = 0.0       # condensate retention fraction (1 -> fully retained)
+    surf_state      = "fixed"    # surface scheme: "mixed_layer" | "fixed" | "skin"
+    surf_albedo     = 0.1       # path to file ("string") or grey quantity (float)
+    albedo_pl       = 0.1   	# Bond albedo (scattering)
+    rayleigh        = true      # enable rayleigh scattering
+    tmp_minimum     = 0.5           # temperature floor on solver
+    tmp_maximum     = 5000.0        # temperature ceiling on solver
+
+    module  = "dummy"           # Which atmosphere module to use
+
+    [atmos_clim.agni]
+        p_top           = 1.0e-5        # bar, top of atmosphere grid pressure
+        spectral_group  = "Frostflow"   # which gas opacities to include
+        spectral_bands  = "48"          # how many spectral bands?
+        num_levels      = 40            # Number of atmospheric grid levels
+        chemistry       = "none"        # "none" | "eq" | "kin"
+
+    [atmos_clim.janus]
+        p_top           = 1.0e-6        # bar, top of atmosphere grid pressure
+        spectral_group  = "Frostflow"   # which gas opacities to include
+        spectral_bands  = "48"          # how many spectral bands?
+        F_atm_bc        = 0             # measure outgoing flux at: (0) TOA | (1) Surface
+        num_levels      = 40           # Number of atmospheric grid levels
+        tropopause      = "none"        # none | skin | dynamic
+
+    [atmos_clim.dummy]
+        gamma           = 0.7           # atmosphere opacity between 0 and 1
+
+# Volatile escape - physics table
+[escape]
+
+    module = "dummy"    # Which escape module to use
+
+    [escape.zephyrus]
+        some_parameter = "some_value"
+
+    [escape.dummy]
+        rate = 2.0e4    #  Bulk unfractionated escape rate [kg s-1]
+
+# Interior - physics table
+[interior]
+    grain_size      = 0.1   # crystal settling grain size [m]
+    F_initial       = 1e6   # Initial heat flux guess [W m-2]
+
+    module = "dummy"   # Which interior module to use
+
+    [interior.spider]
+        num_levels      = 220       # Number of SPIDER grid levels
+        mixing_length   = 2         # Mixing length parameterization
+        tolerance       = 1.0e-10   # solver tolerance
+        tsurf_atol      = 30.0      # tsurf_poststep_change
+        tsurf_rtol      = 0.02      # tsurf_poststep_change_frac
+        ini_entropy     = 2700.0    # Surface entropy conditions [J K-1 kg-1]
+        ini_dsdr        = -4.698e-6 # Interior entropy gradient [J K-1 kg-1 m-1]
+
+    [interior.aragog]
+        some_parameter = "some_value"
+
+# Outgassing - physics table
+[outgas]
+    fO2_shift_IW    = 2         # log10(ΔIW), atmosphere/interior boundary oxidation state
+
+    module = "calliope"         # Which outgassing module to use
+
+    [outgas.calliope]
+        include_H2O  = true     # Include H2O compound
+        include_CO2  = true     # Include CO2 compound
+        include_N2   = true     # Include N2 compound
+        include_S2   = true     # Include S2 compound
+        include_SO2  = true     # Include SO2 compound
+        include_H2   = true     # Include H2 compound
+        include_CH4  = true     # Include CH4 compound
+        include_CO   = true     # Include CO compound
+
+    [outgas.atmodeller]
+        some_parameter = "some_value"
+
+# Volatile delivery - physics table
+[delivery]
+
+    # [Settings here for accretion rate, etc.]
+
+    # Which initial inventory to use?
+    initial = 'elements'        # "elements" | "volatiles"
+
+    # No module for accretion as of yet
+    module = "none"
+
+    # Set initial volatile inventory by planetary element abundances
+    [delivery.elements]
+        CH_ratio    = 1.0       # C/H ratio in mantle/atmosphere system
+        H_oceans    = 6.0       # Hydrogen inventory in units of equivalent Earth oceans, by mass
+        N_ppmw      = 2.0       # Nitrogen inventory in ppmw relative to mantle mass, by mass
+        S_ppmw      = 200.0     # Sulfur inventory in ppmw relative to mass of melt
+
+    # Set initial volatile inventory by partial pressures in atmosphere
+    [delivery.volatiles]
+        H2O  = 0.0          # partial pressure of H2O
+        CO2  = 0.0          # partial pressure of CO2
+        N2   = 0.0          # etc
+        S2   = 0.0
+        SO2  = 0.0
+        H2   = 0.0
+        CH4  = 0.0
+        CO   = 0.0

input/escape.toml

@@ -87,15 +87,14 @@ author  = "Harrison Nicholls, Tim Lichtenberg"
 [star]
 
     # Physical parameters
-    mass    = 1.0       # M_sun
     radius  = 1.0       # R_sun
     Teff    = 5772.0    # K
-    Lbol    = 1.0       # L_sun
+    mass    = 1.0       # M_sun
+    lum_now = 1.0       # L_sun
     omega   = 50.0      # rotation percentile
     age_now = 4.567     # Gyr, current age of star used for scaling
     age_ini = 0.100     # Gyr, model initialisation/start age
 
-
     module  = "mors"
     [star.mors]
         tracks  = "spada"   # evolution tracks: spada | baraffe

input/hd63433d.toml

@@ -87,15 +87,14 @@ author  = "Harrison Nicholls, Tim Lichtenberg"
 [star]
 
     # Physical parameters
-    mass    = 0.99      # M_sun
     radius  = 0.912     # R_sun
     Teff    = 5640.0    # K
-    Lbol    = 0.753     # L_sun
+    mass    = 0.99      # M_sun
+    lum_now = 0.753     # L_sun
     omega   = 50.0      # rotation percentile
     age_now = 4.140     # Gyr, current age of star used for scaling
     age_ini = 0.100     # Gyr, model initialisation/start age
 
-
     module  = "mors"
     [star.mors]
         tracks  = "baraffe"   # evolution tracks: spada | baraffe

input/jgr_grid.toml

@@ -87,15 +87,14 @@ author  = "Harrison Nicholls, Tim Lichtenberg"
 [star]
 
     # Physical parameters
-    mass    = 1.0       # M_sun
     radius  = 1.0       # R_sun
     Teff    = 5772.0    # K
-    Lbol    = 1.0       # L_sun
+    mass    = 1.0       # M_sun
+    lum_now = 1.0       # L_sun
     omega   = 60.0      # rotation percentile
     age_now = 4.567     # Gyr, current age of star used for scaling
     age_ini = 0.100     # Gyr, model initialisation/start age
 
-
     module  = "mors"
     [star.mors]
         tracks  = "spada"   # evolution tracks: spada | baraffe

input/ltt3780b.toml

@@ -87,15 +87,14 @@ author  = "Harrison Nicholls, Tim Lichtenberg"
 [star]
 
     # Physical parameters
-    mass    = 0.401     # M_sun
     radius  = 0.374     # R_sun
     Teff    = 3331.0    # K
-    Lbol    = 0.167     # L_sun
+    mass    = 0.401     # M_sun
+    lum_now = 0.167     # L_sun
     omega   = 20.0      # rotation percentile
     age_now = 3.100     # Gyr, current age of star used for scaling
     age_ini = 0.100     # Gyr, model initialisation/start age
 
-
     module  = "mors"
     [star.mors]
         tracks  = "spada"   # evolution tracks: spada | baraffe

input/t1c.toml

@@ -87,15 +87,14 @@ author  = "Harrison Nicholls, Tim Lichtenberg"
 [star]
 
     # Physical parameters
-    mass    = 0.1       # M_sun
     radius  = 0.1192    # R_sun
     Teff    = 2566.0    # K
-    Lbol    = 0.000553  # L_sun
+    mass    = 0.1       # M_sun
+    lum_now = 0.000553  # L_sun
     omega   = 50.0      # rotation percentile
     age_now = 7.6       # Gyr, current age of star used for scaling
     age_ini = 0.100     # Gyr, model initialisation/start age
 
-
     module  = "mors"
     [star.mors]
         tracks  = "spada"   # evolution tracks: spada | baraffe

src/proteus/config/_compatibility.py

@@ -50,7 +50,7 @@ def _phi_global(config: Config):
     'star_mass': ('star', 'mass'),
     'star_radius_modern': ('star', 'radius'),
     'star_temperature_modern': ('star', 'Teff'),
-    'star_luminosity_modern': ('star', 'Lbol'),
+    'star_luminosity_modern': ('star', 'lum_now'),
     'star_age_modern': ('star', 'age_now'),
     'star_rot_pctle': ('star', 'omega'),
     'star_spectrum': ('star', 'mors', 'spec'),