Merge pull request #343 from FormingWorlds/hn/platon

Synthetic observables with PLATON

.gitignore

@@ -59,6 +59,9 @@ lovepy
 Lovepy
 LOVEPY
 LovePy
+platon
+Platon
+PLATON
 
 # misc
 ######

CONTRIBUTING.md

@@ -2,7 +2,7 @@
 
 ## Development
 
-*PROTEUS* targets Python 3.11 or newer.
+PROTEUS targets Python 3.12 or newer.
 
 Clone the repository into the `proteus` directory:
 

docs/installation.md

@@ -48,9 +48,9 @@ This can be done via brew on MacOS, or with your package manager on Linux. Alter
 If you already have Julia installed, skip this step.
 This should only be done using the official installer, not via your package manager.
 
-    ```console
-    curl -fsSL https://install.julialang.org | sh
-    ```
+```console
+curl -fsSL https://install.julialang.org | sh
+```
 
 ## Download the framework
 
@@ -82,7 +82,7 @@ This should only be done using the official installer, not via your package mana
     The code can be setup in `./socrates/` using the following script.
 
     ```console
-    source tools/get_socrates.sh
+    ./tools/get_socrates.sh
     ```
 
     The environemnt variable `RAD_DIR` must always point to the SOCRATES installation path.
@@ -174,9 +174,23 @@ This should only be done using the official installer, not via your package mana
 Lovepy is written in Julia. You can use the same environment as AGNI if you wish, but you
 should make sure to follow the installation steps below.
 
-    ```console
-    ./tools/get_lovepy.sh
-    ```
+```console
+./tools/get_lovepy.sh
+```
+
+### Synthetic observations calculator (**PLATON**)
+
+[PLATON](https://platon.readthedocs.io/en/latest/intro.html) is a forward modelling and
+retrieval tool for exoplanet atmospheres. In PROTEUS, this tool is used to generate
+synthetic transmission and secondary eclipse observations. To get PLATON and its
+dependencies, use the script below.
+
+```console
+./tools/get_platon.sh
+```
+
+Note that this script will take some time to run; PLATON will need to download
+about 10 GB of opacity data from the internet.
 
 ### Chemical kinetics atmosphere model (**VULCAN**)
 

input/default.toml

@@ -14,6 +14,7 @@
 #   [interior] magma ocean model selection and parameters
 #   [outgas]   outgassing parameters (fO2) and included volatiles
 #   [delivery] initial volatile inventory, and delivery model selection
+#   [observe]  synthetic observations
 
 # ----------------------------------------------------
 # Metadata
@@ -26,7 +27,7 @@ author  = "Harrison Nicholls, Tim Lichtenberg"
     # output files
     [params.out]
         path        = "default"
-        logging     = "INFO"
+        logging     = "DEBUG"
         plot_mod    = 2      # Plotting frequency, 0: wait until completion | n: every n iterations
         plot_fmt    = "png"  # Plotting image file format, "png" or "pdf" recommended
         write_mod   = 1      # Write CSV frequency, 0: wait until completion | n: every n iterations
@@ -274,3 +275,9 @@ author  = "Harrison Nicholls, Tim Lichtenberg"
         H2   = 0.0
         CH4  = 0.0
         CO   = 0.0
+
+# Calculate simulated observations
+[observe]
+
+    # Module with which to calculate the synthetic observables (none, platon)
+    synthesis = "platon"

input/demos/aragog.toml

@@ -274,3 +274,9 @@ author  = "Harrison Nicholls, Tim Lichtenberg"
         H2   = 0.0
         CH4  = 0.0
         CO   = 0.0
+
+# Calculate simulated observations
+[observe]
+
+    # Module with which to calculate the synthetic observables
+    synthesis = "none"

input/demos/dummy.toml

@@ -275,3 +275,9 @@ author  = "Harrison Nicholls, Tim Lichtenberg"
         H2   = 0.0
         CH4  = 0.0
         CO   = 0.0
+
+# Calculate simulated observations
+[observe]
+
+    # Module with which to calculate the synthetic observables
+    synthesis = "none"

input/demos/escape.toml

@@ -275,3 +275,9 @@ author  = "Harrison Nicholls, Tim Lichtenberg"
         H2   = 0.0
         CH4  = 0.0
         CO   = 0.0
+
+# Calculate simulated observations
+[observe]
+
+    # Module with which to calculate the synthetic observables
+    synthesis = "none"

input/planets/earth.toml

@@ -275,3 +275,9 @@ author  = "Harrison Nicholls, Tim Lichtenberg"
         H2   = 0.0
         CH4  = 0.0
         CO   = 0.0
+
+# Calculate simulated observations
+[observe]
+
+    # Module with which to calculate the synthetic observables
+    synthesis = "none"

input/planets/hd63433d.toml

@@ -274,3 +274,9 @@ author  = "Harrison Nicholls, Tim Lichtenberg"
         H2   = 0.0
         CH4  = 0.0
         CO   = 0.0
+
+# Calculate simulated observations
+[observe]
+
+    # Module with which to calculate the synthetic observables
+    synthesis = "none"

input/planets/k218b.toml

@@ -275,3 +275,9 @@ author  = "Harrison Nicholls, Tim Lichtenberg"
         H2   = 0.0
         CH4  = 0.0
         CO   = 0.0
+
+# Calculate simulated observations
+[observe]
+
+    # Module with which to calculate the synthetic observables
+    synthesis = "none"

input/planets/l9859b.toml

@@ -274,3 +274,9 @@ author  = "Harrison Nicholls, Tim Lichtenberg"
         H2   = 0.0
         CH4  = 0.0
         CO   = 0.0
+
+# Calculate simulated observations
+[observe]
+
+    # Module with which to calculate the synthetic observables
+    synthesis = "none"

input/planets/l9859c.toml

@@ -274,3 +274,9 @@ author  = "Harrison Nicholls, Tim Lichtenberg"
         H2   = 0.0
         CH4  = 0.0
         CO   = 0.0
+
+# Calculate simulated observations
+[observe]
+
+    # Module with which to calculate the synthetic observables
+    synthesis = "none"

input/planets/l9859d.toml

@@ -45,7 +45,7 @@ author  = "Harrison Nicholls, Tim Lichtenberg"
 
         [params.dt.adaptive]
             atol         = 0.02  # Step size atol
-            rtol         = 0.07   # Step size rtol
+            rtol         = 0.06   # Step size rtol
 
     # Termination criteria
     #     Set enabled=true/false in each section to enable/disable that termination criterion
@@ -195,7 +195,7 @@ author  = "Harrison Nicholls, Tim Lichtenberg"
     module = "spider"   # Which interior module to use
 
     [interior.spider]
-        num_levels      = 80       # Number of SPIDER grid levels
+        num_levels      = 70       # Number of SPIDER grid levels
         mixing_length   = 2         # Mixing length parameterization
         tolerance       = 1e-6   # solver tolerance
         tsurf_atol      = 5.0      # tsurf_poststep_change
@@ -259,7 +259,7 @@ author  = "Harrison Nicholls, Tim Lichtenberg"
         NH_ratio    = 0.018       # N/H mass ratio in mantle/atmosphere system
         # N_ppmw      = 2.01       # Nitrogen inventory in ppmw relative to mantle mass
 
-        SH_ratio    = 3.8       # S/H mass ratio in mantle/atmosphere system
+        SH_ratio    = 4.0       # S/H mass ratio in mantle/atmosphere system
         # S_ppmw      = 0.0     # Sulfur inventory in ppmw relative to mantle mass
 
     # Set initial volatile inventory by partial pressures in atmosphere
@@ -274,3 +274,9 @@ author  = "Harrison Nicholls, Tim Lichtenberg"
         H2   = 0.0
         CH4  = 0.0
         CO   = 0.0
+
+# Calculate simulated observations
+[observe]
+
+    # Module with which to calculate the synthetic observables
+    synthesis = "platon"

input/planets/trappist1c.toml

@@ -274,3 +274,9 @@ author  = "Harrison Nicholls, Tim Lichtenberg"
         H2   = 0.0
         CH4  = 0.0
         CO   = 0.0
+
+# Calculate simulated observations
+[observe]
+
+    # Module with which to calculate the synthetic observables
+    synthesis = "none"

pyproject.toml

@@ -46,7 +46,7 @@ dependencies = [
     "attrs",
     "cattrs",
     "fwl-janus>=24.11.05",
-    "fwl-mors>=24.11.18",
+    "fwl-mors>=25.02.26",
     "fwl-calliope>=25.02.26",
     "fwl-zephyrus>=24.10.15",
     "aragog>=0.1.9a0",

src/proteus/atmos_clim/wrapper.py

@@ -157,7 +157,7 @@ def run_atmosphere(atmos_o:Atmos_t, config:Config, dirs:dict, loop_counter:dict,
     hf_row["p_xuv"]  = atm_output["p_xuv"]    # Closest pressure to Pxuv    [bar]
     hf_row["R_xuv"]  = atm_output["R_xuv"]    # Radius at p_xuv [m]
 
-    # Calculate observables (measured at infinite distance)
+    # Calculate bolometric observables (measured at infinite distance)
     hf_row["transit_depth"] =  (hf_row["R_obs"]  / hf_row["R_star"])**2.0
     hf_row["contrast_ratio"] = ((hf_row["F_olr"]+hf_row["F_sct"])/hf_row["F_ins"]) * \
                                  (hf_row["R_obs"] / hf_row["separation"])**2.0

src/proteus/config/_config.py

@@ -10,6 +10,7 @@
 from ._delivery import Delivery
 from ._escape import Escape
 from ._interior import Interior
+from ._observe import Observe
 from ._orbit import Orbit
 from ._outgas import Outgas
 from ._params import Params
@@ -30,6 +31,11 @@ def tides_enabled_orbit(instance, attribute, value):
     if (instance.interior.tidal_heat) and (instance.orbit.module is None):
         raise ValueError("Interior tidal heating requires an orbit module to be enabled")
 
+def observe_resolved_atmosphere(instance, attribute, value):
+    # Synthetic observations require a spatially resolved atmosphere profile
+    if (instance.observe.synthesis is not None) and (instance.atmos_clim.module == "dummy"):
+        raise ValueError("Interior tidal heating requires an orbit module to be enabled")
+
 @define
 class Config:
     """Root config parameters.
@@ -58,6 +64,8 @@ class Config:
         Outgassing parameters (fO2, etc) and included volatiles.
     delivery: Delivery
         Initial volatile inventory, and delivery model selection.
+    observe: Observe
+        Synthetic observations.
     """
 
     version: str = field(validator=validators.in_(('2.0',)))
@@ -72,6 +80,7 @@ class Config:
     interior: Interior = field(validator=(tides_enabled_orbit,))
     outgas: Outgas
     delivery: Delivery
+    observe: Observe
 
     def write(self, out:str):
         """

src/proteus/config/_observe.py

@@ -0,0 +1,17 @@
+from __future__ import annotations
+
+from attrs import define, field
+from attrs.validators import in_
+
+from ._converters import none_if_none
+
+
+@define
+class Observe:
+    """Synthetic observations.
+
+    synthesis: str
+        Module to use for calculating synthetic spectra.
+    """
+
+    synthesis: str = field(validator=in_((None,'platon')), converter=none_if_none)

src/proteus/observe/__init__.py

@@ -0,0 +1,5 @@
+from __future__ import annotations
+
+# from .wrapper import run_interior
+
+__all__ = []

src/proteus/observe/common.py

@@ -0,0 +1,10 @@
+from __future__ import annotations
+
+import os
+
+
+def get_transit_fpath(outdir:str):
+    return os.path.join(outdir, "data", "obs_synth_transit.csv")
+
+def get_eclipse_fpath(outdir:str):
+    return os.path.join(outdir, "data", "obs_synth_eclipse.csv")