Tidied things up. Updated plots. Updated cfgs and docs with new param…

…eter.

docs/source/usage.rst

@@ -267,7 +267,13 @@ configuration, but they must all be passed via the config file.
      - Stop the simulation when the atmosphere mass drops below this fraction of its initial mass.
      - False
      - Float
-     - Values between zero and unity.
+     - Values between zero and unity (exclusive).
+
+  * - ``escape_dummy_rate``
+     - Bulk escape rate for dummy escape model [kg s-1]
+     - False
+     - Float
+     - Any reasonable positive value.
 
    * - ``prevent_warming``
      - Flag to ensure that the net upward energy flux is always positive, which prevents the star from causing net heating inside the planet.   

input/default.cfg

@@ -77,6 +77,7 @@ F_crit                      = 0.2       # Critical flux, below which the model w
 # 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            = 0         # Atmosphere model to be used, 0: JANUS | 1: AGNI

input/dummy.cfg

@@ -77,6 +77,7 @@ F_crit                      = 0.2       # Model will terminate when |F_atm| < F_
 # Atmospheric escape 
 escape_model                = 2         # 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           = 2e7       # Bulk escape rate for dummy escape model [kg s-1]
 
 # Method for solving for T(p) profile
 atmosphere_model            = 2         # Atmosphere model to be used, 0: JANUS | 1: AGNI | 2: Dummy

input/janus_mixed.cfg

@@ -77,6 +77,7 @@ F_crit                      = 0.2       # Model will terminate when |F_atm| < F_
 # 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            = 0         # Atmosphere model to be used, 0: JANUS | 1: AGNI

input/jgr_grid.cfg

@@ -77,6 +77,7 @@ F_crit                      = 0.2       # Model will terminate when |F_atm| < F_
 # 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            = 0         # Atmosphere model to be used, 0: JANUS | 1: AGNI

input/rce_mixed.cfg

@@ -77,6 +77,8 @@ F_crit                      = 0.2       # Model will terminate when |F_atm| < F_
 # 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

input/rce_steam.cfg

@@ -77,6 +77,7 @@ F_crit                      = 0.2       # Model will terminate when |F_atm| < F_
 # 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

proteus.py

@@ -410,7 +410,7 @@ def main():
                 esc_result = RunZEPHYRUS()
 
             elif COUPLER_options["escape_model"] == 2:
-                esc_result = RunDummyEsc(hf_row, dt)
+                esc_result = RunDummyEsc(hf_row, dt, COUPLER_options["escape_dummy_rate"])
 
             # store total escape rate 
             hf_row["esc_rate_total"] = esc_result["rate_bulk"]
@@ -419,10 +419,15 @@ def main():
             # update elemental mass targets
             for e in element_list:
                 if e=='O': continue
-                solvevol_target[e] += esc_result[e+"_dm"]
 
-                esc_m  = solvevol_target[e]
-                esc_dm = esc_result[e+"_dm"]
+                # store change, for statistics
+                esc_m  = esc_result[e+"_kg_total"]
+                esc_dm = esc_m - solvevol_target[e]
+
+                # update total elemental inventory
+                solvevol_target[e] = esc_m
+
+                # print info to user
                 log.debug("    escape %s: m=%.2e kg,  dm=%.2e (%.3f%%)"%
                                     (e, esc_m, esc_dm, 100*esc_dm/esc_m))
 

utils/coupler.py

@@ -8,16 +8,17 @@
 
 log = logging.getLogger("PROTEUS")
 
-import plot.cpl_atmosphere as cpl_atmosphere
-import plot.cpl_global as cpl_global
-import plot.cpl_stacked as cpl_stacked
-import plot.cpl_interior as cpl_interior
-import plot.cpl_sflux as cpl_sflux
-import plot.cpl_sflux_cross as cpl_sflux_cross
-import plot.cpl_fluxes_global as cpl_fluxes_global
-import plot.cpl_fluxes_atmosphere as cpl_fluxes_atmosphere
-import plot.cpl_interior_cmesh as cpl_interior_cmesh
-import plot.cpl_observables as cpl_observables
+from plot.cpl_atmosphere import plot_atmosphere
+from plot.cpl_global import plot_global
+from plot.cpl_stacked import plot_stacked
+from plot.cpl_interior import plot_interior
+from plot.cpl_sflux import plot_sflux
+from plot.cpl_sflux_cross import plot_sflux_cross
+from plot.cpl_fluxes_global import plot_fluxes_global
+from plot.cpl_fluxes_atmosphere import plot_fluxes_atmosphere
+from plot.cpl_interior_cmesh import plot_interior_cmesh
+from plot.cpl_observables import plot_observables
+from plot.cpl_elements import plot_elements
 
 def GitRevision(dir:str) -> str:
     '''
@@ -117,8 +118,8 @@ def GetHelpfileKeys():
             "z_obs", "transit_depth", "contrast_ratio", # observed from infinity
 
             # Escape 
-            "esc_rate_total",
-
+            "esc_rate_total", 
+            
             # Atmospheric composition
             "M_atm", "P_surf", "atm_kg_per_mol", # more keys added below
             ]
@@ -272,11 +273,14 @@ def ReadInitFile(init_file_passed:str, verbose=False):
                 if not line.startswith("time_"):
 
                     # Some parameters are int
-                    if key in [ "solid_stop", "steady_stop", "iter_max", "emit_stop", "escape_model",
-                                "plot_iterfreq", "stellar_heating", "mixing_length", "shallow_ocean_layer",
-                                "atmosphere_chemistry", "solvevol_use_params", "insert_rscatter", "water_cloud",
-                                "tropopause", "F_atm_bc", "atmosphere_solve_energy", "atmosphere_surf_state",
-                                "dt_dynamic", "prevent_warming", "atmosphere_model", "atmosphere_nlev"]:
+                    if key in [ "solid_stop", "steady_stop", "iter_max", "emit_stop", 
+                                "escape_model", "atmosphere_surf_state", "water_cloud",
+                                "plot_iterfreq", "stellar_heating", "mixing_length", 
+                                "atmosphere_chemistry", "solvevol_use_params", 
+                                "tropopause", "F_atm_bc", "atmosphere_solve_energy", 
+                                "dt_dynamic", "prevent_warming", "atmosphere_model", 
+                                "atmosphere_nlev", "insert_rscatter", 
+                                "shallow_ocean_layer", "SEPARATION"]:
                         val = int(val)
 
                     # Some are str
@@ -365,15 +369,22 @@ def UpdatePlots( output_dir, COUPLER_options, end=False, num_snapshots=7):
     """
 
 
+
+    # Check model configuration
+    dummy_atm = bool(COUPLER_options["atmosphere_model"] == 2)
+    escape    = bool(COUPLER_options["escape_model"] > 0)
+
+
     # Get all JSON files
     output_times = get_all_output_times( output_dir )
 
     # Global properties for all timesteps
-    if len(output_times) > 1:
-        cpl_global.plot_global(output_dir, COUPLER_options)   
+    if len(output_times) > 2:
+        plot_global(output_dir, COUPLER_options)   
 
-    # Check if we are using the dummy atmosphere
-    dummy_atm = (COUPLER_options["atmosphere_model"] == 2)
+        # Elemental mass inventory
+        if escape:
+            plot_elements(output_dir, COUPLER_options["plot_format"])
 
     # Filter to JSON files with corresponding NetCDF files
     if not dummy_atm:
@@ -402,25 +413,24 @@ def UpdatePlots( output_dir, COUPLER_options, end=False, num_snapshots=7):
     plot_times = sorted(set(plot_times)) # Remove any duplicates + resort
     log.debug("Snapshots to plot:" + str(plot_times))
 
-    # Specific timesteps for paper plots
-    cpl_interior.plot_interior(output_dir, plot_times, COUPLER_options["plot_format"])     
+    # Temperature profiles
+    plot_interior(output_dir, plot_times, COUPLER_options["plot_format"])     
     if not dummy_atm:
-        cpl_atmosphere.plot_atmosphere(output_dir, plot_times, COUPLER_options["plot_format"])
-        cpl_stacked.plot_stacked(output_dir, plot_times, COUPLER_options["plot_format"])
+        plot_atmosphere(output_dir, plot_times, COUPLER_options["plot_format"])
+        plot_stacked(output_dir, plot_times, COUPLER_options["plot_format"])
 
         if COUPLER_options["atmosphere_model"] != 1:
             # don't make this plot for AGNI, since it will do it itself
-            cpl_fluxes_atmosphere.plot_fluxes_atmosphere(output_dir, COUPLER_options["plot_format"])
-
+            plot_fluxes_atmosphere(output_dir, COUPLER_options["plot_format"])
 
     # Only at the end of the simulation
     if end:
-        cpl_global.plot_global(output_dir, COUPLER_options, logt=False)   
-        cpl_interior_cmesh.plot_interior_cmesh(output_dir, plot_format=COUPLER_options["plot_format"])
-        cpl_sflux.plot_sflux(output_dir, plot_format=COUPLER_options["plot_format"])
-        cpl_sflux_cross.plot_sflux_cross(output_dir, plot_format=COUPLER_options["plot_format"])
-        cpl_fluxes_global.plot_fluxes_global(output_dir, COUPLER_options)
-        cpl_observables.plot_observables(output_dir, plot_format=COUPLER_options["plot_format"])
+        plot_global(output_dir, COUPLER_options, logt=False)   
+        plot_interior_cmesh(output_dir, plot_format=COUPLER_options["plot_format"])
+        plot_sflux(output_dir, plot_format=COUPLER_options["plot_format"])
+        plot_sflux_cross(output_dir, plot_format=COUPLER_options["plot_format"])
+        plot_fluxes_global(output_dir, COUPLER_options)
+        plot_observables(output_dir, plot_format=COUPLER_options["plot_format"])
 
     # Close all figures
     plt.close()

utils/escape.py

@@ -7,7 +7,7 @@
 log = logging.getLogger("PROTEUS")
 
 
-def RunDummyEsc(hf_row:dict, dt:float):
+def RunDummyEsc(hf_row:dict, dt:float, phi_bulk:float):
     """Run dummy escape model.
 
     Parameters
@@ -16,43 +16,40 @@ def RunDummyEsc(hf_row:dict, dt:float):
             Dictionary of helpfile variables, at this iteration only
         dt : float 
             Time interval over which escape is occuring [yr]
+        phi_bulk : float 
+            Bulk escape rate [kg s-1]
 
     Returns
     ----------
         esc_result : dict 
-            Dictionary of elemental mass deltas [kg]
+            Dictionary of updated total elemental mass inventories [kg]
 
     """
     log.info("Running dummy escape...")
 
-    # Hardcoded dummy value of bulk volatile escape rate [kg/s]
-    phi = 2e7
-
     # store value
     out = {}
-    out["rate_bulk"] = phi
+    out["rate_bulk"] = phi_bulk
 
-    # calculate total mass of volatiles
+    # calculate total mass of volatiles (except oxygen, which is set by fO2)
     M_vols = 0.0
     for e in element_list:
         if e=='O': continue 
         M_vols += hf_row[e+"_kg_total"]
 
+
     # for each elem, calculate new total inventory while
     # maintaining a constant mass mixing ratio
     for e in element_list:
         if e=='O': continue
 
-        # current elemental mass ratio in atmosphere 
+        # current elemental mass ratio in total 
         emr = hf_row[e+"_kg_total"]/M_vols
 
         log.debug("    %s mass ratio = %.2e "%(e,emr))
 
-        # new atmosphere mass of element e, keeping a constant mixing ratio of that element 
-        e_atm = emr * (M_vols - phi * dt * secs_per_year)
-
-        # calculate change in total mass of element e
-        out[e+"_dm"] = e_atm - hf_row[e+"_kg_total"]
+        # new total mass of element e, keeping a constant mixing ratio of that element 
+        out[e+"_kg_total"] = emr * (M_vols - phi_bulk * dt * secs_per_year)
 
     return out