Merge sulfur fixes and plotting updates. Downloads stellar spectra fr…

…om OSF
FormingWorlds · Jul 18, 2024 · 2f8bdb6 · 2f8bdb6
1 parent 4bcb47f
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diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-## JANUS (temperature structure generator)
+## JANUS (1D convective atmosphere model)
 
 Generates a temperature profile using the generalised moist pseudoadiabat and a prescribed stratosphere. Calculates radiative fluxes using SOCRATES.   
 

diff --git a/examples/SocRadConv.py b/examples/SocRadConv.py
@@ -21,7 +21,7 @@
 from importlib.resources import files
 
 from janus.modules import RadConvEqm, plot_fluxes, plot_emission
-from janus.utils import atmos, CleanOutputDir, DownloadSpectralFiles, plot_adiabats, ReadBandEdges, StellarSpectrum
+from janus.utils import atmos, CleanOutputDir, DownloadSpectralFiles, DownloadStellarSpectra, plot_adiabats, ReadBandEdges, StellarSpectrum
 import mors
 
 ####################################
@@ -70,7 +70,7 @@
 
     #Download required spectral files
     DownloadSpectralFiles("/Dayspring")
-    DownloadSpectralFiles("/stellar_spectra")
+    DownloadStellarSpectra()
 
     # Move/prepare spectral file
     print("Inserting stellar spectrum")

diff --git a/examples/demo_instellation.py b/examples/demo_instellation.py
@@ -12,7 +12,7 @@
 import numpy as np
 
 from janus.modules import MCPA_CBL
-from janus.utils import atmos, CleanOutputDir, DownloadSpectralFiles, ReadBandEdges, StellarSpectrum
+from janus.utils import atmos, CleanOutputDir, DownloadSpectralFiles, DownloadStellarSpectra, ReadBandEdges, StellarSpectrum
 
 import mors
 
@@ -37,7 +37,7 @@
 
     #Download required spectral files
     DownloadSpectralFiles("/Oak")
-    DownloadSpectralFiles("/stellar_spectra")
+    DownloadStellarSpectra()
 
     # Setup spectral file
     print("Inserting stellar spectrum")

diff --git a/examples/demo_runaway_greenhouse.py b/examples/demo_runaway_greenhouse.py
@@ -11,7 +11,7 @@
 from importlib.resources import files
 
 from janus.modules import RadConvEqm
-from janus.utils import atmos, CleanOutputDir, DownloadSpectralFiles, ReadBandEdges, StellarSpectrum
+from janus.utils import atmos, CleanOutputDir, DownloadSpectralFiles, DownloadStellarSpectra, ReadBandEdges, StellarSpectrum
 import mors
 
 if __name__=='__main__':
@@ -36,7 +36,7 @@
 
     #Download required spectral files
     DownloadSpectralFiles("/Oak")
-    DownloadSpectralFiles("/stellar_spectra")
+    DownloadStellarSpectra()
 
     # Setup spectral file
     print("Inserting stellar spectrum")

diff --git a/src/janus/modules/plot_flux_balance.py b/src/janus/modules/plot_flux_balance.py
@@ -16,180 +16,30 @@
 from janus.modules.spectral_planck_surface import surf_Planck_nu
 import janus.utils.GeneralAdiabat as ga # Moist adiabat with multiple condensibles
 
-
-def plot_flux_balance(atm_dry, atm_moist, cp_dry, time, dirs):
-
-    fig, ((ax1, ax2), (ax3, ax4)) = plt.subplots(2, 2, figsize=(13,10))
-    # sns.set_style("ticks")
-    # sns.despine()
-
-    # Line settings
-    col_idx  = 3
-    col_vol1 = "H2O"
-    col_vol2 = "N2"
-    col_vol3 = "H2"
-    col_vol4 = "O2"
-
-    # Temperature vs. pressure
-    ax1.semilogy(atm_moist.tmp,atm_moist.p, color=ga.vol_colors[col_vol1][col_idx+1], ls="-", label=r'Moist adiabat')
-    if cp_dry == True: ax1.semilogy(atm_dry.tmp,atm_dry.p, color=ga.vol_colors[col_vol3][col_idx+1], ls="-", label=r'Dry adiabat')
-    ax1.legend()
-    ax1.invert_yaxis()
-    ax1.set_xlabel(r'Temperature $T$ (K)')
-    ax1.set_ylabel(r'Pressure $P$ (Pa)')
-    # ax1.set_ylim(bottom=atm_moist.ps*1.01)
-    ax1.set_ylim(top=atm_moist.ptop, bottom=atm_moist.ps)
-
-    # Print active species
-    active_species = r""
-    for vol in atm_moist.vol_list:
-        if atm_moist.vol_list[vol] > 1e-5:
-            active_species = active_species + ga.vol_latex[vol] + ", "
-    active_species = active_species[:-2]
-    ax1.text(0.02, 0.02, r"Active species: "+active_species, va="bottom", ha="left", fontsize=10, transform=ax1.transAxes, bbox=dict(fc='white', ec="white", alpha=0.5, boxstyle='round', pad=0.1), color=ga.vol_colors["black_1"] )
-
-    # Fluxes vs. pressure
-
-    # Zero line
-    ax2.axvline(0, color=ga.vol_colors["qgray_light"], lw=0.5)
-    # ax2.axvline(-1e+3, color=ga.vol_colors["qgray_light"], lw=0.5)
-    # ax2.axvline(1e+3, color=ga.vol_colors["qgray_light"], lw=0.5)
-
-    # SW down / instellation flux
-    if cp_dry == True: ax2.semilogy(atm_dry.SW_flux_down*(-1),atm_dry.pl, color=ga.vol_colors[col_vol3][col_idx], ls=":")
-    ax2.semilogy(atm_moist.SW_flux_down*(-1),atm_moist.pl, color=ga.vol_colors[col_vol2][col_idx], ls=":", label=r'$F_{\odot}^{\downarrow}$')
-
-    # LW down / thermal downward flux
-    if cp_dry == True: ax2.semilogy(atm_dry.LW_flux_down*(-1),atm_dry.pl, color=ga.vol_colors[col_vol3][col_idx], ls="--")
-    ax2.semilogy(atm_moist.LW_flux_down*(-1),atm_moist.pl, color=ga.vol_colors[col_vol2][col_idx+1], ls="--", label=r'$F_\mathrm{t}^{\downarrow}$')
-    # ls=(0, (3, 1, 1, 1))
-
-    # Thermal upward flux, total
-    if cp_dry == True: ax2.semilogy(atm_dry.flux_up_total,atm_dry.pl, color=ga.vol_colors[col_vol3][col_idx], ls="--")
-    ax2.semilogy(atm_moist.flux_up_total,atm_moist.pl, color=ga.vol_colors[col_vol1][col_idx], ls="--", label=r'$F_\mathrm{t}^{\uparrow}$')
-
-    # Net flux
-    if cp_dry == True: ax2.semilogy(atm_dry.net_flux,atm_dry.pl, color=ga.vol_colors[col_vol3][6], ls="-", lw=2)
-    ax2.semilogy(atm_moist.net_flux,atm_moist.pl, color=ga.vol_colors[col_vol1][6], ls="-", lw=2, label=r'$F_\mathrm{net}^{\uparrow}$')
-
-    # # SW up
-    # if cp_dry == True: ax2.semilogy(atm_dry.SW_flux_up,atm_dry.pl, color=ga.vol_colors[col_vol3][col_idx], ls=":")
-    # ax2.semilogy(atm_moist.SW_flux_up,atm_moist.pl, color=ga.vol_colors[col_vol1][col_idx], ls=":", label=r'$F_\mathrm{SW}^{\uparrow}$')
-
-    # # LW up
-    # if cp_dry == True: ax2.semilogy(atm_dry.LW_flux_up,atm_dry.pl, color=ga.vol_colors[col_vol3][col_idx], ls=(0, (5, 1)))
-    # ax2.semilogy(atm_moist.LW_flux_up,atm_moist.pl, color=ga.vol_colors[col_vol1][col_idx], ls=(0, (5, 1)), label=r'$F_\mathrm{LW}^{\uparrow}$')
-
-    ax2.legend(ncol=6, fontsize=10, loc=3)
-    ax2.invert_yaxis()
-    ax2.set_xscale("symlog") # https://stackoverflow.com/questions/3305865/what-is-the-difference-between-log-and-symlog
-    ax2.set_xlabel(r'Outgoing flux $F^{\uparrow}$ (W m$^{-2}$)')
-    ax2.set_ylabel(r'Pressure $P$ (Pa)')
-    ax2.set_ylim(top=atm_moist.ptop, bottom=atm_moist.ps)
-
-    # Wavenumber vs. OLR
-    ax3.plot(atm_moist.band_centres, surf_Planck_nu(atm_moist)/atm_moist.band_widths, color="gray",ls='--',label=str(round(atm_moist.ts))+' K blackbody')
-    if cp_dry == True: ax3.plot(atm_dry.band_centres, atm_dry.net_spectral_flux[:,0]/atm_dry.band_widths, color=ga.vol_colors[col_vol3][col_idx])
-    ax3.plot(atm_moist.band_centres, atm_moist.net_spectral_flux[:,0]/atm_moist.band_widths, color=ga.vol_colors[col_vol1][col_idx+1])
-    ax3.set_ylabel(r'Spectral flux density (W m$^{-2}$ cm$^{-1}$)')
-    ax3.set_xlabel(r'Wavenumber (cm$^{-1}$)')
-    ax3.legend(loc=1)
-    ymax_plot = 1.2*np.max(atm_moist.net_spectral_flux[:,0]/atm_moist.band_widths)
-    ax3.set_ylim(bottom=0, top=ymax_plot)
-    ax3.set_xlim(left=0, right=np.max(np.where(atm_moist.net_spectral_flux[:,0]/atm_moist.band_widths > ymax_plot/1000., atm_moist.band_centres, 0.)))
-    # ax3.set_xlim(left=0, right=30000)
-
-
-    # Heating versus pressure
-    ax4.axvline(0, color=ga.vol_colors["qgray_light"], lw=0.5)
-
-    if cp_dry == True: 
-        ax4.plot(atm_dry.LW_heating, atm_dry.p, ls="--", color=ga.vol_colors[col_vol3][col_idx+1])
-        ax4.plot(atm_dry.net_heating, atm_dry.p, lw=2, color=ga.vol_colors[col_vol3][col_idx+1])
-        ax4.plot(atm_dry.SW_heating, atm_dry.p, ls=":", color=ga.vol_colors[col_vol3][col_idx+1])
-
-    ax4.plot(atm_moist.LW_heating, atm_moist.p, ls="--", color=ga.vol_colors[col_vol1][col_idx+1], label=r'LW')
-    ax4.plot(atm_moist.net_heating, atm_moist.p, lw=2, color=ga.vol_colors[col_vol1][col_idx+1], label=r'Net')
-    ax4.plot(atm_moist.SW_heating, atm_moist.p, ls=":", color=ga.vol_colors[col_vol1][col_idx+1], label=r'SW')
-
-    # Plot tropopause
-    trpp_idx = int(atm_moist.trppidx)
-    if trpp_idx > 0:
-        ax4.axhline(atm_moist.pl[trpp_idx], color=ga.vol_colors[col_vol2][col_idx], lw=1.0, ls="-.", label=r'Tropopause')
-
-    ax4.invert_yaxis()
-    ax4.legend(ncol=4, fontsize=10, loc=3)
-    ax4.set_ylabel(r'Pressure $P$ (Pa)')
-    ax4.set_xlabel(r'Heating (K/day)')
-    # ax4.set_xscale("log")
-    ax4.set_yscale("log") 
-    x_minmax = np.max([abs(np.min(atm_moist.net_heating[10:])), abs(np.max(atm_moist.net_heating[10:]))])
-    x_minmax = np.max([ 20, x_minmax ])
-    if not math.isnan(x_minmax):
-        ax4.set_xlim(left=-x_minmax, right=x_minmax)
-    ax4.set_ylim(top=atm_moist.ptop, bottom=atm_moist.ps)
-    # ax4.set_yticks([1e-10, 1e-5, 1e0, 1e5])
-    # ax4.set_xticks([0.1, 0.3, 1, 3, 10, 30, 100])
-    # ax4.set_xticklabels(["0.1", "0.3", "1", "3", "10", "30", "100"])
-
-    # # Wavelength versus OLR log plot
-    # OLR_cm_moist = atm_moist.LW_spectral_flux_up[:,0]/atm_moist.band_widths
-    # wavelength_moist  = [ 1e+4/i for i in atm_moist.band_centres ]          # microns
-    # OLR_micron_moist  = [ 1e+4*i for i in OLR_cm_moist ]                    # microns
-    # if cp_dry == True: 
-    #     OLR_cm_dry = atm_dry.LW_spectral_flux_up[:,0]/atm_dry.band_widths
-    #     wavelength_dry  = [ 1e+4/i for i in atm_dry.band_centres ]              # microns
-    #     OLR_micron_dry  = [ 1e+4*i for i in OLR_cm_dry ]                        # microns
-    #     ax4.plot(wavelength_dry, OLR_micron_dry, color=ga.vol_colors[col_vol3][col_idx+1])
-
-    # ax4.plot(wavelength_moist, OLR_micron_moist, color=ga.vol_colors[col_vol1][col_idx+1])
-    # ax4.set_ylabel(r'Spectral flux density (W m$^{-2}$ $\mu$m$^{-1}$)')
-    # ax4.set_xlabel(r'Wavelength $\lambda$ ($\mu$m)')
-    # ax4.set_xscale("log")
-    # ax4.set_yscale("log") 
-    # ax4.set_xlim(left=0.1, right=100)
-    # ax4.set_ylim(bottom=1e-20, top=1e5)
-    # # ax4.set_yticks([1e-10, 1e-5, 1e0, 1e5])
-    # ax4.set_xticks([0.1, 0.3, 1, 3, 10, 30, 100])
-    # ax4.set_xticklabels(["0.1", "0.3", "1", "3", "10", "30", "100"])
-
-    fig.savefig(dirs["output"]+"/"+"TP_"+str(round(time["planet"]))+'.pdf', bbox_inches="tight")
-    plt.close(fig)
-
-    # with open(dirs["output"]+"/"+str(int(time["planet"]))+"_atm.pkl", "wb") as atm_file: 
-    #     pkl.dump(atm, atm_file, protocol=pkl.HIGHEST_PROTOCOL)
-
-    # # Save atm object to .json file
-    # json_atm = json.dumps(atm.__dict__)
-    # with open(dirs["output"]+"/"+str(int(time_current))+"_atm.json", "wb") as atm_file:
-    #     json.dump(json_atm, atm_file)
-
-
 # Plotting
 def plot_fluxes(atm,filename='output/fluxes.pdf'):
 
     fig,ax = plt.subplots()
 
     ax.axvline(0,color='black',lw=0.8)
 
-    # for p in np.logspace(-6, 3, 80)*1.0e5:
-    #     ax.axhline(y=p, color='purple', lw=1, alpha=0.3)
+    arr_p = atm.pl*1e-5
 
-    ax.plot(atm.flux_up_total,atm.pl,color='red',label='UP',lw=1)
-    ax.plot(atm.SW_flux_up   ,atm.pl,color='red',label='UP SW',linestyle='dotted',lw=2)
-    ax.plot(atm.LW_flux_up   ,atm.pl,color='red',label='UP LW',linestyle='dashed',lw=1)
+    ax.plot(atm.flux_up_total,arr_p,color='red',label='UP',lw=1)
+    ax.plot(atm.SW_flux_up   ,arr_p,color='red',label='UP SW',linestyle='dotted',lw=2)
+    ax.plot(atm.LW_flux_up   ,arr_p,color='red',label='UP LW',linestyle='dashed',lw=1)
 
-    ax.plot(-1.0*atm.flux_down_total,atm.pl,color='green',label='DN',lw=2)
-    ax.plot(-1.0*atm.SW_flux_down   ,atm.pl,color='green',label='DN SW',linestyle='dotted',lw=3)
-    ax.plot(-1.0*atm.LW_flux_down   ,atm.pl,color='green',label='DN LW',linestyle='dashed',lw=2)
+    ax.plot(-1.0*atm.flux_down_total,arr_p,color='green',label='DN',lw=2)
+    ax.plot(-1.0*atm.SW_flux_down   ,arr_p,color='green',label='DN SW',linestyle='dotted',lw=3)
+    ax.plot(-1.0*atm.LW_flux_down   ,arr_p,color='green',label='DN LW',linestyle='dashed',lw=2)
 
-    ax.plot(atm.net_flux ,atm.pl,color='black',label='NET')
+    ax.plot(atm.net_flux ,arr_p,color='black',label='NET')
 
     ax.set_xlabel("Upward-directed flux [W m-2]")
     ax.set_xscale("symlog")
     ax.set_ylabel("Pressure [Pa]")
     ax.set_yscale("log")
-    ax.set_ylim([atm.pl[-1],atm.pl[0]])
+    ax.set_ylim(top=np.amin(arr_p)/1.5, bottom=np.amax(arr_p)*1.5)
 
     ax.legend(loc='upper left')
 

diff --git a/src/janus/utils/GeneralAdiabat.py b/src/janus/utils/GeneralAdiabat.py
@@ -33,17 +33,19 @@
 # https://chrisalbon.com/python/data_visualization/seaborn_color_palettes/
 no_colors   = 7
 vol_colors = {
-    "H2O"            : [mpl.colormaps["PuBu"](i) for i in np.linspace(0,1.0,no_colors)],
-    "CO2"            : [mpl.colormaps["Reds"](i) for i in np.linspace(0,1.0,no_colors)],
-    "H2"             : [mpl.colormaps["Greens"](i) for i in np.linspace(0,1.0,no_colors)],
-    "N2"             : [mpl.colormaps["Purples"](i) for i in np.linspace(0,1.0,no_colors)],
     "O2"             : [mpl.colormaps["Wistia"](i) for i in np.linspace(0,1.0,no_colors+2)],
     "O3"             : [mpl.colormaps["spring"](i) for i in np.linspace(0,1.0,no_colors+2)],
-    "CH4"            : [mpl.colormaps["RdPu"](i) for i in np.linspace(0,1.0,no_colors)],
-    "CO"             : [mpl.colormaps["pink_r"](i) for i in np.linspace(0,1.0,no_colors)],
     "S"              : [mpl.colormaps["YlOrBr"](i) for i in np.linspace(0,1.0,no_colors)],
-    "He"             : [mpl.colormaps["Greys"](i) for i in np.linspace(0,1.0,no_colors)],
-    "NH3"            : [mpl.colormaps["summer"](i) for i in np.linspace(0,1.0,no_colors)],
+    "H2O": "#027FB1",
+    "CO2": "#D24901",
+    "H2" : "#008C01",
+    "CH4": "#C720DD",
+    "CO" : "#D1AC02",
+    "N2" : "#870036",
+    "S2" : "#FF8FA1",
+    "SO2": "#00008B",
+    "He" : "#30FF71",
+    "NH3": "#675200",
     "mixtures"       : [mpl.colormaps["Set3"](i) for i in np.linspace(0,1.0,no_colors)],
     "H2O-CO2"        : mpl.colormaps["Set3"](1.0/no_colors),
     "CO2-H2O"        : mpl.colormaps["Set3"](1.0/no_colors),
@@ -943,17 +945,17 @@ def plot_adiabats(atm,filename='output/general_adiabat.pdf'):
 
             # Saturation vapor pressure for given temperature
             Psat_array = [ p_sat(vol, T,water_lookup=atm.water_lookup) for T in T_sat_array ]
-            ax1.semilogy( T_sat_array, Psat_array, label=r'$p_\mathrm{sat}$'+vol_latex[vol], lw=ls_ind, ls=":", color=vol_colors[vol][4])
+            ax1.semilogy( T_sat_array, Psat_array, label=r'$p_\mathrm{sat}$'+vol_latex[vol], lw=ls_ind, ls=":", color=vol_colors[vol])
 
             # Plot partial pressures
-            ax1.semilogy(atm.tmp, atm.p_vol[vol], color=vol_colors[vol][4], lw=ls_ind, ls="-", label=r'$p$'+vol_latex[vol],alpha=0.99)
+            ax1.semilogy(atm.tmp, atm.p_vol[vol], color=vol_colors[vol], lw=ls_ind, ls="-", label=r'$p$'+vol_latex[vol],alpha=0.99)
 
             # Sum up partial pressures
             p_partial_sum += atm.p_vol[vol]
 
             # Plot individual molar concentrations
-            ax2.semilogy(atm.x_cond[vol],atm.p, color=vol_colors[vol][4], lw=ls_ind, ls="--", label=vol_latex[vol]+" cond.")
-            ax2.semilogy(atm.x_gas[vol],atm.p, color=vol_colors[vol][4], lw=ls_ind, ls="-", label=vol_latex[vol]+" gas")
+            ax2.semilogy(atm.x_cond[vol],atm.p, color=vol_colors[vol], lw=ls_ind, ls="--", label=vol_latex[vol]+" cond.")
+            ax2.semilogy(atm.x_gas[vol],atm.p, color=vol_colors[vol], lw=ls_ind, ls="-", label=vol_latex[vol]+" gas")
 
     # # Plot sum of partial pressures as check
     ax1.semilogy(atm.tmp, p_partial_sum, color="green", lw=ls_dry, ls="--", label=r'$\sum p^\mathrm{i}$',alpha=0.99)

diff --git a/src/janus/utils/data.py b/src/janus/utils/data.py
@@ -1,17 +1,13 @@
 import os
 from osfclient.api import OSF
 
-#project ID of the stellar evolution tracks folder in the OSF
-project_id = 'vehxg'
-
 basic_list =[
         "/Dayspring/256",
         "/Frostflow/256",
         "/Legacy",
         "/Mallard",
         "/Oak",
-        "/Reach",
-        "/stellar_spectra"
+        "/Reach"
         ]
 
 def download_folder(storage, folder_name, local_path):
@@ -33,6 +29,31 @@ def download_folder(storage, folder_name, local_path):
                 file.write_to(local_file)
     return
 
+
+def GetFWLData():
+    fwl_data_dir = os.getenv('FWL_DATA')
+    if os.environ.get("FWL_DATA") == None:
+        raise Exception("The FWL_DATA environment variable where spectral data will be downloaded needs to be set up!")
+    return fwl_data_dir
+
+def DownloadStellarSpectra():
+    #project ID of the stellar spectra on OSF 
+    project_id = '8r2sw'
+
+    # Link with OSF project repository
+    osf = OSF()
+    project = osf.project(project_id)
+    storage = project.storage('osfstorage')
+
+    # Folder
+    data_dir = GetFWLData() + "/stellar_spectra"
+    if not os.path.exists(data_dir):
+        os.makedirs(data_dir)
+
+    # Get all named spectra
+    download_folder(storage,"/Named",data_dir)
+
+
 def DownloadSpectralFiles(fname="",nband=256):
     ''''
     Download spectral files data
@@ -44,13 +65,11 @@ def DownloadSpectralFiles(fname="",nband=256):
                                 (only relevant for Dayspring, Frostflow and Honeyside)
     '''
 
-    #Check if data environment variable is set up
-    fwl_data_dir = os.getenv('FWL_DATA')
-    if os.environ.get("FWL_DATA") == None:
-        raise Exception("The FWL_DATA environment variable where spectral data will be downloaded needs to be set up!")
+    #project ID of the spectral files on OSF 
+    project_id = 'vehxg'
 
     #Create spectral file data repository if not existing
-    data_dir = fwl_data_dir + "/spectral_files"
+    data_dir = GetFWLData() + "/spectral_files"
     if not os.path.exists(data_dir):
         os.makedirs(data_dir)
 

diff --git a/src/janus/utils/phys.py b/src/janus/utils/phys.py
@@ -76,7 +76,9 @@
         "NO"  : 0.0300061, 
         "NO2" : 0.0460055, 
         "HNO3": 0.06301284, 
-        "OCS" : 0.060075       
+        "OCS" : 0.060075,       
+        "S2"  : 0.0641,               # kg mol-1
+
     }
 
 #This class allows convenient access

diff --git a/tests/test_instellation.py b/tests/test_instellation.py
@@ -5,7 +5,7 @@
 import numpy as np
 
 from janus.modules import MCPA_CBL
-from janus.utils import atmos, CleanOutputDir, DownloadSpectralFiles, ReadBandEdges, StellarSpectrum
+from janus.utils import atmos, CleanOutputDir, DownloadSpectralFiles, DownloadStellarSpectra, ReadBandEdges, StellarSpectrum
 import mors
 
 def test_instellation():
@@ -27,7 +27,7 @@ def test_instellation():
 
     #Download required spectral files
     DownloadSpectralFiles("/Oak")
-    DownloadSpectralFiles("/stellar_spectra")
+    DownloadStellarSpectra()
 
     # Setup spectral file
     print("Inserting stellar spectrum")