Merge pull request #114 from FormingWorlds/observational

Some observational quantities

examples/earth_demo/init_coupler.cfg

@@ -57,10 +57,7 @@ dt_initial                  = 1e4    # 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
-F_eps                       = 1.0       # W m-2
-F_diff                      = 0.1       # flux fraction
 RF_crit                     = 0.01      # depth fraction
-dTs_atm                     = 30        # K
 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

input/rce_mixed.cfg

@@ -11,7 +11,7 @@ star_age_modern             = 4.567e9             # yr, age of star (TODAY)
 star_spectrum               = stellar_spectra/Named/sun.txt   # Stellar spectrum file at 1 AU (TODAY)
 
 ##### Planet configuration
-mean_distance               = 1.0       # AU, star-planet distance
+mean_distance               = 0.4       # AU, star-planet distance
 mass                        = 5.972e24  # kg, planet mass--original mass of the Earth
 radius                      = 6.371e6   # m, planet surface radius
 
@@ -124,7 +124,7 @@ tsurf_poststep_change_frac  = 0.01
 planet_coresize             = 0.55
 
 # Initial entropy conditions for interior
-ic_adiabat_entropy          = 2650.0
+ic_adiabat_entropy          = 2750.0
 ic_dsdr                     = -4.698e-06
 
 # Atmosphere heat flux start guess, adjusted during runtime [W/m^2]
@@ -137,7 +137,7 @@ fO2_shift_IW                = 0
 solvevol_use_params          = 1
 
 # Parameters used to solve for initial partial pressures (when solvepp_use_params = 1)
-T_magma                     = 2300      # Surface temperature initial guess [K]
+T_magma                     = 3000      # Surface temperature initial guess [K]
 Phi_global                  = 1.0       # Mantle melt fraction initial guess
 CH_ratio                    = 1.0       # C/H ratio
 hydrogen_earth_oceans       = 10.0      # Hydrogen inventory in units of equivalent Earth oceans

plot/cpl_observables.py

@@ -0,0 +1,70 @@
+#!/usr/bin/env python3
+
+from utils.modules_ext import *
+from utils.plot import *
+
+log = logging.getLogger("PROTEUS")
+
+def plot_observables( output_dir, plot_format="pdf", t0=100.0):
+
+    log.info("Plot observables")
+
+    hf_all = pd.read_csv(output_dir+"/runtime_helpfile.csv", sep=r"\s+")
+
+    time = np.array(hf_all["Time"] )
+    if len(time) < 3:
+        log.warning("Cannot make plot with less than 3 samples")
+        return
+
+    # make plot
+    lw = 1.2
+    scale = 1.1
+    fig,axl = plt.subplots(1,1, figsize=(7*scale,4*scale))
+
+    # left axis 
+    axl.plot(time, hf_all["transit_depth"]*1e6, lw=lw, color='k')    
+    axl.set_ylabel("Transit depth [ppm]")
+
+    # right axis 
+    axr = axl.twinx()
+    color = "tab:red"
+    axr.plot(time, hf_all["contrast_ratio"]*1e9, lw=lw, color=color)    
+    axr.set_ylabel("Contrast ratio [ppb]")
+    axr.yaxis.label.set_color(color)
+    axr.tick_params(axis='y', colors=color)
+
+    # x-axis
+    axl.set_xlabel("Time [yr]")
+    axl.set_xscale("log")
+    axl.set_xlim(left=t0, right=np.amax(time))
+    axl.grid(alpha=0.2)
+
+    plt.close()
+    plt.ioff()
+
+    fpath = os.path.join(output_dir, "plot_observables.%s"%plot_format)
+    fig.savefig(fpath, dpi=200, bbox_inches='tight')
+
+#====================================================================
+def main():
+
+    if len(sys.argv) == 2:
+        cfg = sys.argv[1]
+    else:
+        cfg = 'init_coupler.cfg' 
+
+    # Read in COUPLER input file
+    log.info("Read cfg file")
+    from utils.coupler import ReadInitFile, SetDirectories
+    COUPLER_options, time_dict = ReadInitFile( cfg )
+
+    # Set directories dictionary
+    dirs = SetDirectories(COUPLER_options)
+
+    plot_observables( output_dir=dirs["output"], plot_format=COUPLER_options["plot_format"] )
+
+#====================================================================
+
+if __name__ == "__main__":
+
+    main()

proteus.py

@@ -11,7 +11,7 @@
 from utils.coupler import *
 from utils.spider import RunSPIDER
 from utils.surface_gases import *
-from utils.logs import SetupLogger, GetLogfilePath, GetCurrentLogfileIndex
+from utils.logs import SetupLogger, GetLogfilePath, GetCurrentLogfileIndex, StreamToLogger
 
 from janus.utils.StellarSpectrum import PrepareStellarSpectrum,InsertStellarSpectrum
 from janus.utils import DownloadSpectralFiles, DownloadStellarSpectra
@@ -404,7 +404,6 @@ def main():
                 hf_row[k] = solvevol_result[k]
         ############### / OUTGASSING
 
-
 
         ############### UPDATE TIME 
 
@@ -450,13 +449,17 @@ def main():
 
 
         # Store atmosphere module output variables
+        hf_row["z_obs"]  = atm_output["z_obs"] 
         hf_row["F_atm"]  = atm_output["F_atm"] 
         hf_row["F_olr"]  = atm_output["F_olr"] 
         hf_row["F_sct"]  = atm_output["F_sct"] 
         hf_row["T_surf"] = atm_output["T_surf"]
         hf_row["F_net"]  = hf_row["F_int"] - hf_row["F_atm"]
-
-        ############### / ATMOSPHERE SUB-LOOP
+
+        # Calculate observables (measured at infinite distance)
+        hf_row["transit_depth"] =  (hf_row["z_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["z_obs"] / (COUPLER_options["mean_distance"]*AU))**2.0
 
         # Update full helpfile
         if loop_counter["total"]>1:

utils/agni.py

@@ -332,6 +332,9 @@ def RunAGNI(loops_total:int, dirs:dict, COUPLER_options:dict, hf_row:dict):
     net_flux =      np.array(ds.variables["fl_N"][:])
     LW_flux_up =    np.array(ds.variables["fl_U_LW"][:])
     SW_flux_up =    np.array(ds.variables["fl_U_SW"][:])
+    arr_p =         np.array(ds.variables["p"][:])
+    arr_z =         np.array(ds.variables["z"][:])
+    radius =        float(ds.variables["planet_radius"][:])
     T_surf =        float(ds.variables["tmp_surf"][:])
     ds.close()
 
@@ -348,11 +351,16 @@ def RunAGNI(loops_total:int, dirs:dict, COUPLER_options:dict, hf_row:dict):
     log.info("SOCRATES fluxes (net@BOA, net@TOA, OLR): %.3f, %.3f, %.3f W/m^2" % 
                                         (net_flux[-1], net_flux[0] ,LW_flux_up[0]))
 
+    # find 1 mbar level 
+    idx = find_nearest(arr_p*1e5, 1e-3)[1]
+    z_obs = arr_z[idx]
+
     output = {}
     output["F_atm"]  = F_atm_new
     output["F_olr"]  = LW_flux_up[0]
     output["F_sct"]  = SW_flux_up[0]
     output["T_surf"] = T_surf
+    output["z_obs"]  = z_obs + radius
 
     return output
 

utils/coupler.py

@@ -17,6 +17,7 @@
 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
 
 def GitRevision(dir:str) -> str:
     '''
@@ -86,8 +87,7 @@ def CreateLockFile(output_dir:str):
     keepalive_file = os.path.join(output_dir,"keepalive")
     safe_rm(keepalive_file)
     with open(keepalive_file, 'w') as fp:
-        fp.write("Removing this file will be interpreted by PROTEUS as a \
-                        request to stop the simulation loop\n")
+        fp.write("Removing this file will be interpreted by PROTEUS as a request to stop the simulation loop\n")
     return keepalive_file
 
 def GetHelpfileKeys():
@@ -113,6 +113,9 @@ def GetHelpfileKeys():
             # Stellar 
             "R_star", "age_star",
 
+            # Observational 
+            "z_obs", "transit_depth", "contrast_ratio", # observed from infinity
+
             # Surface composition
             "P_surf", "atm_kg_per_mol", # more keys are added below
 
@@ -415,6 +418,7 @@ def UpdatePlots( output_dir, COUPLER_options, end=False, num_snapshots=7):
         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"])
 
     # Close all figures
     plt.close()

utils/dummy_atmosphere.py

@@ -103,5 +103,6 @@ def _resid(x):
     output["F_atm"] =  F_atm_lim             # Net flux at TOA
     output["F_olr"] =  fluxes["fl_U_LW"]     # OLR
     output["F_sct"] =  fluxes["fl_U_SW"]     # Scattered SW flux
+    output["z_obs"] =  COUPLER_options["radius"]
 
     return output

utils/janus.py

@@ -242,11 +242,16 @@ def RunJANUS( atm, time:float, dirs:dict, COUPLER_options:dict, hf_all:pd.DataFr
 
     # Restore stdout
     sys.stdout , sys.stderr = old_stdout , old_stderr
+
+    # find 1 mbar level 
+    idx = find_nearest(atm.p*1e5, 1e-3)[1]
+    z_obs = atm.z[idx]
 
     output["T_surf"] = atm.ts            # Surface temperature [K]
     output["F_atm"]  = F_atm_lim         # Net flux at TOA
     output["F_olr"]  = atm.LW_flux_up[0] # OLR
     output["F_sct"]  = atm.SW_flux_up[0] # Scattered SW flux
+    output["z_obs"]  = z_obs + atm.planet_radius
 
     return output