Display information on module versions, remove PROTEUS.env

.github/workflows/tests.yaml

@@ -64,7 +64,6 @@ jobs:
 
       - name: Test with pytest
         run: |
-          source PROTEUS.env
           coverage run -m pytest
 
       - name: Upload PNG plots as artifacts

CITATION.cff

@@ -32,7 +32,7 @@ authors:
   orcid: "https://orcid.org/0000-0002-0673-4860"
 
 title: "PROTEUS"
-version: 24.07.25
+version: 24.10.30
 doi: 10.xx/xx.xx
-date-released: 2024-07-19
+date-released: 2024-10-30
 url: "https://github.com/FormingWorlds/PROTEUS"

docs/installation.md

@@ -127,7 +127,13 @@ You will need to setup Python (>=3.10) on your system. This can be done via brew
     ./tools/get_petsc.sh
     ```
 
-8. Setup PROTEUS coupled framework
+8. Setup interior evolution model (**SPIDER**)
+
+    ```console
+    ./tools/get_spider.sh
+    ```
+
+9. Setup PROTEUS coupled framework
 
     1. Get the remaining Python dependencies
 
@@ -139,19 +145,6 @@ You will need to setup Python (>=3.10) on your system. This can be done via brew
 
         - The variable `RAD_DIR` must point to the SOCRATES installation path. It is best to add this to your shell rc file.
 
-        - Setup other variables
-
-            ```console
-            source PROTEUS.env
-            ```
-            This file can also be added to your shell rc file.
-
-9. Setup interior evolution model (**SPIDER**)
-
-    ```console
-    ./tools/get_spider.sh
-    ```
-
 10. Done! 🚀
     Any remaining dependencies will be downloaded when the model is first run.
 

input/aragog.toml

@@ -123,19 +123,19 @@ author  = "Harrison Nicholls, Tim Lichtenberg"
 
 # Atmosphere - physics table
 [atmos_clim]
-    prevent_warming = true      # do not allow the planet to heat up
+    prevent_warming = false      # 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_greyalbedo  = 0.1      # surface grey albedo
     albedo_pl       = 0.0   	# Bond albedo (scattering)
-    rayleigh        = true      # enable rayleigh scattering
+    rayleigh        = false      # enable rayleigh scattering
     tmp_minimum     = 0.5           # temperature floor on solver
     tmp_maximum     = 5000.0        # temperature ceiling on solver
 
-    module  = "janus"           # Which atmosphere module to use
+    module  = "dummy"           # Which atmosphere module to use
 
     [atmos_clim.agni]
         p_top           = 1.0e-5        # bar, top of atmosphere grid pressure
@@ -156,7 +156,7 @@ author  = "Harrison Nicholls, Tim Lichtenberg"
         tropopause      = "none"        # none | skin | dynamic
 
     [atmos_clim.dummy]
-        gamma           = 0.7           # atmosphere opacity between 0 and 1
+        gamma           = 0.8           # atmosphere opacity between 0 and 1
 
 # Volatile escape - physics table
 [escape]
@@ -188,7 +188,7 @@ author  = "Harrison Nicholls, Tim Lichtenberg"
 
     [interior.aragog]
         num_levels      = 100       # Number of Aragog grid levels
-        tolerance       = 1.0e-8   # solver tolerance
+        tolerance       = 1.0e-7   # solver tolerance
 
 # Outgassing - physics table
 [outgas]

input/default.toml

@@ -26,8 +26,8 @@ author  = "Harrison Nicholls, Tim Lichtenberg"
     # output files
     [params.out]
         path        = "default"
-        logging     = "DEBUG"
-        plot_mod    = 1      # Plotting frequency, 0: wait until completion | n: every n iterations
+        logging     = "INFO"
+        plot_mod    = 2      # Plotting frequency, 0: wait until completion | n: every n iterations
         plot_fmt    = "pdf"  # Plotting image file format, "png" or "pdf" recommended
 
     # time-stepping

input/hd63433d.toml

@@ -90,10 +90,10 @@ author  = "Harrison Nicholls, Tim Lichtenberg"
     mass    = 0.99      # M_sun
     age_ini = 0.100     # Gyr, model initialisation/start age
 
-    module  = "mors"
+    module  = "dummy"
     [star.mors]
         rot_pctle = 50.0    # rotation percentile
-        tracks  = "baraffe" # evolution tracks: spada | baraffe
+        tracks  = "spada" # evolution tracks: spada | baraffe
         age_now = 0.414     # Gyr, current age of star used for scaling
         spec    = "stellar_spectra/Named/sun.txt" # stellar spectrum
 
@@ -139,21 +139,21 @@ author  = "Harrison Nicholls, Tim Lichtenberg"
 
     [atmos_clim.agni]
         p_top           = 1.0e-5        # bar, top of atmosphere grid pressure
-        spectral_group  = "Dayspring"   # which gas opacities to include
-        spectral_bands  = "16"         # how many spectral bands?
+        spectral_group  = "Honeyside"   # which gas opacities to include
+        spectral_bands  = "256"         # how many spectral bands?
         num_levels      = 55            # Number of atmospheric grid levels
-        chemistry       = "eq"        # "none" | "eq"
+        chemistry       = "none"        # "none" | "eq"
         surf_material   = "greybody"    # surface material file for scattering
         solution_atol   = 2e-3          # solver absolute tolerance
         solution_rtol   = 5e-2          # solver relative tolerance
 
     [atmos_clim.janus]
-        p_top           = 1.0e-6        # bar, top of atmosphere grid pressure
+        p_top           = 1.0e-5        # bar, top of atmosphere grid pressure
         spectral_group  = "Honeyside"   # which gas opacities to include
         spectral_bands  = "256"         # how many spectral bands?
         F_atm_bc        = 0             # measure outgoing flux at: (0) TOA | (1) Surface
-        num_levels      = 80            # Number of atmospheric grid levels
-        tropopause      = "skin"        # none | skin | dynamic
+        num_levels      = 90            # Number of atmospheric grid levels
+        tropopause      = "none"        # none | skin | dynamic
 
     [atmos_clim.dummy]
         gamma           = 0.7           # atmosphere opacity between 0 and 1