FormingWorlds · nichollsh · Sep 10, 2024 · Sep 5, 2024 · Sep 6, 2024 · Sep 6, 2024
diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
@@ -21,7 +21,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.10']
+        python-version: ['3.10', '3.12']
 
     env:
       FWL_DATA: /home/runner/work/fwl_data

diff --git a/.gitignore b/.gitignore
@@ -33,6 +33,9 @@ JANUS
 agni
 Agni
 AGNI
+calliope
+Calliope
+CALLIOPE
 
 # misc
 ######

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -22,3 +22,5 @@ repos:
         types_or: [python, pyi]
       # - id: ruff-format
       #   types_or: [python, pyi]
+
+exclude: 'examples/.*'
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -10,5 +10,6 @@
     ],
     "python.analysis.exclude": [
         "**/__pycache__", "petsc", ".git", "SPIDER"
-    ]
+    ],
+    "julia.environmentPath": "${workspaceFolder}/AGNI"
 }
diff --git a/docs/installation.md b/docs/installation.md
@@ -123,6 +123,13 @@ You will need to setup Python (>=3.10) on your system. This can be done via brew
         pip install -e JANUS/.
         ```
 
+    - CALLIOPE outgassing model
+
+        ```console
+        git clone [email protected]:FormingWorlds/CALLIOPE
+        pip install -e CALLIOPE/.
+        ```
+
 9. Setup PROTEUS coupled framework
 
     - Get the remaining Python dependencies

diff --git a/examples/dummy/init_coupler.toml b/examples/dummy/init_coupler.toml
@@ -26,7 +26,7 @@ P_top                       = 1.0e-6    # bar, Pressure at TOA
 ##### PROTEUS settings
 
 iter_max                    = 9000
-log_level                   = 'DEBUG'
+log_level                   = 'INFO'
 
 # Output subdirectory name (relative to output folder)
 dir_output                  = 'dummy'

diff --git a/examples/dummy/plot_elements.png b/examples/dummy/plot_elements.png
diff --git a/examples/dummy/plot_escape.png b/examples/dummy/plot_escape.png
diff --git a/examples/dummy/plot_fluxes_global.png b/examples/dummy/plot_fluxes_global.png
diff --git a/examples/dummy/plot_global_lin.png b/examples/dummy/plot_global_lin.png
diff --git a/examples/dummy/plot_global_log.png b/examples/dummy/plot_global_log.png
diff --git a/examples/dummy/plot_interior.png b/examples/dummy/plot_interior.png
diff --git a/examples/dummy/plot_interior_cmesh.png b/examples/dummy/plot_interior_cmesh.png
diff --git a/examples/dummy/plot_observables.png b/examples/dummy/plot_observables.png
diff --git a/examples/dummy/plot_sflux.png b/examples/dummy/plot_sflux.png
diff --git a/examples/dummy/proteus_00.log b/examples/dummy/proteus_00.log
diff --git a/examples/dummy/runtime_helpfile.csv b/examples/dummy/runtime_helpfile.csv
diff --git a/examples/earth_demo/plot_atmosphere.pdf b/examples/earth_demo/plot_atmosphere.pdf
diff --git a/examples/earth_demo/plot_emission.pdf b/examples/earth_demo/plot_emission.pdf
diff --git a/examples/earth_demo/plot_fluxes_atmosphere.pdf b/examples/earth_demo/plot_fluxes_atmosphere.pdf
diff --git a/examples/earth_demo/plot_fluxes_global.pdf b/examples/earth_demo/plot_fluxes_global.pdf
diff --git a/examples/earth_demo/plot_global_lin.pdf b/examples/earth_demo/plot_global_lin.pdf
diff --git a/examples/earth_demo/plot_global_log.pdf b/examples/earth_demo/plot_global_log.pdf
diff --git a/examples/earth_demo/plot_interior.pdf b/examples/earth_demo/plot_interior.pdf
diff --git a/examples/earth_demo/plot_interior_cmesh.pdf b/examples/earth_demo/plot_interior_cmesh.pdf
diff --git a/examples/earth_demo/plot_observables.pdf b/examples/earth_demo/plot_observables.pdf
diff --git a/examples/earth_demo/plot_sflux.pdf b/examples/earth_demo/plot_sflux.pdf
diff --git a/examples/earth_demo/plot_stacked.pdf b/examples/earth_demo/plot_stacked.pdf
diff --git a/examples/earth_demo/proteus_00.log b/examples/earth_demo/proteus_00.log
diff --git a/examples/earth_demo/runtime_helpfile.csv b/examples/earth_demo/runtime_helpfile.csv
diff --git a/examples/hd63433d/init_coupler.toml b/examples/hd63433d/init_coupler.toml
@@ -0,0 +1,170 @@
+########## PROTEUS configuration file
+
+##### Star configuration
+
+star_model                  = 1                 # Evolution model to use for star (0: Spada, 1: Baraffe)
+star_mass                   = 0.99                # M_sun, mass of star
+star_radius_modern          = 0.912                 # R_sun, radius of star (TODAY)
+star_temperature_modern     = 5640.0             # K, temperature of star (TODAY)
+star_luminosity_modern      = 0.753                 # L_sun, luminosity of star (TODAY) used for Baraffe model
+star_age_modern             = 4.14e8             # yr, age of star (TODAY)
+star_rot_pctle              = 50.0
+star_spectrum               = 'stellar_spectra/Named/sun.txt'   # Stellar spectrum file at 1 AU (TODAY)
+
+##### Planet configuration
+mean_distance               = 0.0503       # AU, star-planet distance
+mass                        = 1.0         # M_earth
+radius                      = 1.073         # R_earth
+
+zenith_angle                = 54.74    # Tidally locked [Hamano+15,  acos(1/sqrt(3)) ]
+asf_scalefactor             = 0.25     # absorbed solar flux scale factor = 1/4
+albedo_s                    = 0.2 		# surface albedo
+albedo_pl                   = 0.0   	# Bond albedo (scattering)
+
+P_top                       = 1.0e-5    # bar, Pressure at TOA
+
+##### PROTEUS settings
+
+iter_max                    = 9000
+log_level                   = 'DEBUG'
+
+# Output subdirectory name (relative to output folder)
+dir_output                  = 'hd63433d'
+
+# Choose times
+time_star                   = 50.0e6  	# yr, time since star formation
+time_target                 = 4.567e+9  # yr, target time for MO evolution
+
+# SOCRATES spectral file to use (relative to FWL_DATA folder)
+spectral_file               = 'spectral_files/Dayspring/256/Dayspring.sf'
+
+# Stellar heating toggle, 0: disabled | 1: enabled
+stellar_heating             = 1
+
+# Time-stepping stuff
+plot_iterfreq               = 1     # Plotting frequency, 0: wait until completion | n: every n iterations
+plot_format                 = 'png'  # Plotting image file format
+sspec_dt_update             = 3e6    # Time intervals at which to re-calculate the stellar spectrum
+sinst_dt_update             = 1e2    # Time intervals at which to re-calculate the instellation
+dt_maximum                  = 1e7    # Maximum time-step
+dt_minimum                  = 3e2    # Minimum time-step
+dt_method                   = 1      # Time-stepping method, 0: proportional | 1: adaptive | 2: maximum
+dt_propconst                = 52.0   # Proportionality constant for dt_method=0
+dt_atol                     = 0.02  # Step size atol
+dt_rtol                     = 0.07   # Step size rtol
+dt_initial                  = 1e3    # Inital step size
+
+# Flux convergence scheme and tolerances for surface equilibration
+shallow_ocean_layer         = 0         # 0: off | 1: on
+F_atm_bc                    = 0         # Boundary condition choice for F_atm, 0: TOA | 1: Surface
+skin_d                      = 0.01      # m
+skin_k                      = 2.0       # W m-1 K-1
+prevent_warming             = 1         # Require that the planet only cool down over time, 0: disabled | 1: enabled
+
+# Break at solidification?
+solid_stop                  = 1
+phi_crit                    = 0.005     # melt fraction
+
+# Break at steady state?
+steady_stop                 = 1
+steady_flux                 = 0.8        # Maximum absolute value of F_atm allowed for convergence
+steady_dprel                = 3.0e-9     # Percentage change in melt fraction over time (dp/p)/dt*100
+
+# Break at small flux?
+emit_stop                   = 1         # Enable this break condition
+F_crit                      = 0.1       # Model will terminate when |F_atm| < F_crit
+
+# Atmospheric escape
+escape_model                = 0         # Escape model to be used, 0: None | 1: ZEPHYRUS | 2: Dummy
+escape_stop                 = 3e-4      # Terminate when atm mass drops below this fraction of its initial mass
+escape_dummy_rate           = 0.0       # Bulk escape rate for dummy escape model [kg s-1]
+
+
+# Method for solving for T(p) profile
+atmosphere_model            = 1         # Atmosphere model to be used, 0: JANUS | 1: AGNI
+atmosphere_surf_state       = 2         # Atmosphere bottom edge boundary condition, 0: free | 1: fixed at T_surf | 2: conductive skin
+
+# Number of levels
+atmosphere_nlev             = 40
+
+# Temperature limits throughout atmosphere [K]
+min_temperature             = 0.5
+max_temperature             = 5000.0
+
+# Clouds
+water_cloud                 = 0         # enable water cloud radiative effects? (1: yes, 0: no)
+alpha_cloud                 = 0.0       # condensate retention fraction (1 -> fully retained)
+
+# Tropopause type, 0: none | 1: skin temperature | 2: dynamic
+tropopause                  = 1
+
+# Rayleigh scattering, 0: Disabled | 1: Enabled
+rayleigh                    = 1
+
+# Atmospheric chemistry, 0: Disabled | 1: Equilibrium | 2: Kinetics
+atmosphere_chemistry       = 0
+
+##### SPIDER-specific settings
+
+interior_nlev               = 290
+grain_size                  = 0.1
+
+# Mixing length parameterization: 1: variable | 2: constant
+mixing_length               = 2
+
+# Standard tolerance for solvers
+solver_tolerance            = 1.0e-10
+
+# Maximum absolute surface temperature change [K]
+tsurf_poststep_change       = 20.0
+
+# Maximum fractional surface temperature change [fraction]
+tsurf_poststep_change_frac  = 0.01
+
+# Fractional core radius
+planet_coresize             = 0.55
+
+# Initial entropy conditions for interior
+ic_adiabat_entropy          = 3200.0
+ic_dsdr                     = -4.698e-06
+
+# Atmosphere heat flux start guess, adjusted during runtime [W/m^2]
+F_atm                       = 1e5
+
+# Oxygen fugacity offset relative to the IW buffer (log10 units)
+fO2_shift_IW                = 0
+
+# Enable solving for initial partial pressures (0: off | 1: on)
+solvevol_use_params          = 1
+
+# Parameters used to solve for initial partial pressures (when solvepp_use_params = 1)
+Phi_global                  = 1.0       # Mantle melt fraction initial guess
+CH_ratio                    = 1.0       # C/H ratio
+hydrogen_earth_oceans       = 8.0      # Hydrogen inventory in units of equivalent Earth oceans
+nitrogen_ppmw               = 2.0       # Nitrogen inventory in ppmw relative to mantle mass
+sulfur_ppmw                 = 300.0     # Sulfur inventory in ppmw relative to mass of melt
+
+# Prescribed injected partial pressures [bar]
+H2O_included                = 1
+H2O_initial_bar             = 0.0
+
+CO2_included                = 1
+CO2_initial_bar             = 0.0
+
+N2_included                 = 1
+N2_initial_bar              = 0.0
+
+S2_included                 = 1
+S2_initial_bar              = 0.0
+
+SO2_included                = 1
+SO2_initial_bar             = 0.0
+
+H2_included                 = 1
+H2_initial_bar              = 0.0
+
+CH4_included                = 1
+CH4_initial_bar             = 0.0
+
+CO_included                 = 1
+CO_initial_bar              = 0.0
diff --git a/examples/hd63433d/plot_atmosphere.png b/examples/hd63433d/plot_atmosphere.png
diff --git a/examples/hd63433d/plot_emission.png b/examples/hd63433d/plot_emission.png
diff --git a/examples/hd63433d/plot_fluxes_atmosphere.png b/examples/hd63433d/plot_fluxes_atmosphere.png
diff --git a/examples/hd63433d/plot_fluxes_global.png b/examples/hd63433d/plot_fluxes_global.png
diff --git a/examples/hd63433d/plot_global_lin.png b/examples/hd63433d/plot_global_lin.png
diff --git a/examples/hd63433d/plot_global_log.png b/examples/hd63433d/plot_global_log.png
diff --git a/examples/hd63433d/plot_interior.png b/examples/hd63433d/plot_interior.png
diff --git a/examples/hd63433d/plot_interior_cmesh.png b/examples/hd63433d/plot_interior_cmesh.png
diff --git a/examples/hd63433d/plot_observables.png b/examples/hd63433d/plot_observables.png
diff --git a/examples/hd63433d/plot_sflux.png b/examples/hd63433d/plot_sflux.png
diff --git a/examples/hd63433d/plot_sflux_cross.png b/examples/hd63433d/plot_sflux_cross.png
diff --git a/examples/hd63433d/plot_stacked.png b/examples/hd63433d/plot_stacked.png
diff --git a/examples/hd63433d/plot_vmr.png b/examples/hd63433d/plot_vmr.png
-Original file line number
+Diff line change
@@ Expand Up / @@ -33,6 +33,9 @@ JANUS @@
     agni
     Agni
     AGNI
+    calliope
+    Calliope
+    CALLIOPE
     # misc
     ######
@@ Expand Down @@