From 4224d0446769182effee05fc7cebccfa3a9283d9 Mon Sep 17 00:00:00 2001 From: Laurent Soucasse <135331272+lsoucasse@users.noreply.github.com> Date: Thu, 11 Jul 2024 11:31:33 +0200 Subject: [PATCH 1/4] Update the DownloadSpectralFile function such that it only downloads data if the corresponding local repository does not exist. --- src/janus/utils/data.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/janus/utils/data.py b/src/janus/utils/data.py index af018ac..a1a4e32 100644 --- a/src/janus/utils/data.py +++ b/src/janus/utils/data.py @@ -62,16 +62,16 @@ def DownloadSpectralFiles(fname="",nband=256): #If no folder specified download all basic list if not fname: for folder in basic_list: - print(folder) - download_folder(storage,folder,data_dir) + if not os.path.exists(data_dir+folder): + download_folder(storage,folder,data_dir) elif fname in ["/Dayspring","/Frostflow","/Honeyside"]: - print("HERE ") folder = fname + "/" + str(nband) - print(folder) - download_folder(storage,folder,data_dir) + if not os.path.exists(data_dir+folder): + download_folder(storage,folder,data_dir) elif fname in ["/Kynesgrove","/Legacy","/Mallard","/Oak","/Reach","/stellar_spectra"]: folder = fname - download_folder(storage,folder,data_dir) + if not os.path.exists(data_dir+folder): + download_folder(storage,folder,data_dir) else: print("Unrecognised folder name in DownloadSpectralFiles") From 4b29e30ac0c257b12e484815385b79d8c6c99d9d Mon Sep 17 00:00:00 2001 From: Laurent Soucasse <135331272+lsoucasse@users.noreply.github.com> Date: Thu, 11 Jul 2024 12:43:41 +0200 Subject: [PATCH 2/4] Create shortcut to access Janus functions. --- src/janus/modules/__init__.py | 8 ++++++++ src/janus/utils/__init__.py | 18 ++++++++++++++++++ 2 files changed, 26 insertions(+) diff --git a/src/janus/modules/__init__.py b/src/janus/modules/__init__.py index e69de29..fd318ac 100644 --- a/src/janus/modules/__init__.py +++ b/src/janus/modules/__init__.py @@ -0,0 +1,8 @@ +#Main Janus solvers +from .solve_pt import RadConvEqm, MCPA, MCPA_CBL + +#Plot fluxes +from .plot_flux_balance import plot_fluxes + +#Plot emission +from .plot_emission_spectrum import plot_emission diff --git a/src/janus/utils/__init__.py b/src/janus/utils/__init__.py index e69de29..7ffc2b9 100644 --- a/src/janus/utils/__init__.py +++ b/src/janus/utils/__init__.py @@ -0,0 +1,18 @@ + +# The atmosphere class +from .atmosphere_column import * + +# Data download +from .data import DownloadSpectralFiles + +# Socrates utility module +from .socrates import CleanOutputDir + +# Stellar Spectrum utilities +from .StellarSpectrum import InsertStellarSpectrum + +# Read spectral file +from .ReadSpectralFile import ReadBandEdges + +#General adiabat module +from .GeneralAdiabat import plot_adiabats From 738f2c5f8220322faad4b5b8d87976caf48424f5 Mon Sep 17 00:00:00 2001 From: Laurent Soucasse <135331272+lsoucasse@users.noreply.github.com> Date: Thu, 11 Jul 2024 13:20:46 +0200 Subject: [PATCH 3/4] Update Janus examples to use Mors for stellar instellation. --- examples/SocRadConv.py | 23 ++++++++--------------- examples/demo_instellation.py | 20 +++++++++----------- examples/demo_runaway_greenhouse.py | 17 +++++++---------- 3 files changed, 24 insertions(+), 36 deletions(-) diff --git a/examples/SocRadConv.py b/examples/SocRadConv.py index 3c00373..e95446a 100755 --- a/examples/SocRadConv.py +++ b/examples/SocRadConv.py @@ -20,18 +20,9 @@ import numpy as np from importlib.resources import files -from janus.modules.stellar_luminosity import InterpolateStellarLuminosity -from janus.modules.solve_pt import RadConvEqm -from janus.modules.solve_pt import * -from janus.modules.plot_flux_balance import plot_fluxes -from janus.modules.plot_emission_spectrum import plot_emission -from janus.utils.socrates import CleanOutputDir - -import janus.utils.GeneralAdiabat as ga # Moist adiabat with multiple condensibles -from janus.utils.atmosphere_column import atmos -import janus.utils.StellarSpectrum as StellarSpectrum -from janus.utils.ReadSpectralFile import ReadBandEdges -from janus.utils.data import DownloadSpectralFiles +from janus.modules import RadConvEqm, plot_fluxes, plot_emission +from janus.utils import atmos, CleanOutputDir, DownloadSpectralFiles, plot_adiabats, ReadBandEdges, StellarSpectrum +import mors #################################### ##### Stand-alone initial conditions @@ -44,7 +35,7 @@ if os.environ.get('RAD_DIR') == None: raise Exception("Socrates environment variables not set! Have you installed Socrates and sourced set_rad_env?") 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!") + raise Exception("The FWL_DATA environment variable where spectral and evolution tracks data will be downloaded needs to be set up!") dirs = { "janus": str(files("janus"))+"/", "output": os.path.abspath(os.getcwd())+"/output/" @@ -98,7 +89,9 @@ if cfg['star']['stellar_heating'] == False: atm.instellation = 0. else: - atm.instellation = InterpolateStellarLuminosity(star_mass, time, mean_distance) + mors.DownloadEvolutionTracks("/Baraffe") + baraffe = mors.BaraffeTrack(star_mass) + atm.instellation = baraffe.BaraffeSolarConstant(time['star'], mean_distance) print("Instellation:", round(atm.instellation), "W/m^2") # Set up atmosphere with general adiabat @@ -118,7 +111,7 @@ ) # Plot abundances w/ TP structure - ga.plot_adiabats(atm,filename= dirs["output"]+"moist_ga.png") + plot_adiabats(atm,filename= dirs["output"]+"moist_ga.png") atm.write_PT(filename= dirs["output"]+"moist_pt.tsv") atm.write_ncdf( dirs["output"]+"moist_atm.nc") plot_fluxes(atm,filename= dirs["output"]+"moist_fluxes.png") diff --git a/examples/demo_instellation.py b/examples/demo_instellation.py index 9d35d7f..5b7c97b 100755 --- a/examples/demo_instellation.py +++ b/examples/demo_instellation.py @@ -11,14 +11,10 @@ import os, shutil, toml import numpy as np -from janus.modules.stellar_luminosity import InterpolateStellarLuminosity -from janus.modules.solve_pt import * -from janus.utils.socrates import CleanOutputDir -from janus.utils.atmosphere_column import atmos -import janus.utils.StellarSpectrum as StellarSpectrum -import janus.utils.phys as phys -from janus.utils.ReadSpectralFile import ReadBandEdges -from janus.utils.data import DownloadSpectralFiles +from janus.modules import MCPA_CBL +from janus.utils import atmos, CleanOutputDir, DownloadSpectralFiles, ReadBandEdges, StellarSpectrum + +import mors if __name__=='__main__': @@ -28,7 +24,7 @@ if os.environ.get('RAD_DIR') == None: raise Exception("Socrates environment variables not set! Have you installed Socrates and sourced set_rad_env?") 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!") + raise Exception("The FWL_DATA environment variable where spectral and evolution tracks data will be downloaded needs to be set up!") dirs = { "janus": str(files("janus"))+"/", "output": os.path.abspath(os.getcwd())+"/output/" @@ -57,9 +53,11 @@ with open(cfg_file, 'r') as f: cfg = toml.load(f) - # Planet + # Star luminosity time = { "planet": cfg['planet']['time'], "star": cfg['star']['time']} star_mass = cfg['star']['star_mass'] + mors.DownloadEvolutionTracks("/Baraffe") + baraffe = mors.BaraffeTrack(star_mass) # Define volatiles by mole fractions vol_mixing = { @@ -88,7 +86,7 @@ for i in range(7): print("Orbital separation = %.2f AU" % r_arr[i]) - atm.instellation = InterpolateStellarLuminosity(star_mass, time, r_arr[i]) + atm.instellation = baraffe.BaraffeSolarConstant(time['star'], r_arr[i]) atmos.setTropopauseTemperature(atm) atm = MCPA_CBL(dirs, atm, False, rscatter = True, T_surf_max=9.0e99, T_surf_guess = atm.trppT+100) diff --git a/examples/demo_runaway_greenhouse.py b/examples/demo_runaway_greenhouse.py index 348b6de..b870f5b 100755 --- a/examples/demo_runaway_greenhouse.py +++ b/examples/demo_runaway_greenhouse.py @@ -10,14 +10,9 @@ from matplotlib.ticker import MultipleLocator from importlib.resources import files -from janus.modules.stellar_luminosity import InterpolateStellarLuminosity -from janus.modules.solve_pt import RadConvEqm -from janus.utils.socrates import CleanOutputDir - -from janus.utils.atmosphere_column import atmos -import janus.utils.StellarSpectrum as StellarSpectrum -from janus.utils.ReadSpectralFile import ReadBandEdges -from janus.utils.data import DownloadSpectralFiles +from janus.modules import RadConvEqm +from janus.utils import atmos, CleanOutputDir, DownloadSpectralFiles, ReadBandEdges, StellarSpectrum +import mors if __name__=='__main__': @@ -28,7 +23,7 @@ if os.environ.get('RAD_DIR') == None: raise Exception("Socrates environment variables not set! Have you installed Socrates and sourced set_rad_env?") 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!") + raise Exception("The FWL_DATA environment variable where spectral and evolution tracks data will be downloaded needs to be set up!") dirs = { "janus": str(files("janus"))+"/", "output": os.path.abspath(os.getcwd())+"/output/" @@ -72,7 +67,9 @@ atm = atmos.from_file(cfg_file, band_edges, vol_mixing=vol_mixing, vol_partial={}) # Compute stellar heating - atm.instellation = InterpolateStellarLuminosity(star_mass, time, mean_distance) + mors.DownloadEvolutionTracks("/Baraffe") + baraffe = mors.BaraffeTrack(star_mass) + atm.instellation = baraffe.BaraffeSolarConstant(time['star'], mean_distance) #Run Janus From f5259683fa703628cda378c83c74308b08a8bd57 Mon Sep 17 00:00:00 2001 From: Laurent Soucasse <135331272+lsoucasse@users.noreply.github.com> Date: Fri, 12 Jul 2024 09:54:27 +0200 Subject: [PATCH 4/4] Update test and remove old luminosity track data/functions. --- pyproject.toml | 3 +- src/janus/data/luminosity_tracks/Lum_m0.1.txt | 433 ------------------ src/janus/data/luminosity_tracks/Lum_m0.2.txt | 433 ------------------ src/janus/data/luminosity_tracks/Lum_m0.4.txt | 433 ------------------ src/janus/data/luminosity_tracks/Lum_m0.6.txt | 433 ------------------ src/janus/data/luminosity_tracks/Lum_m0.8.txt | 433 ------------------ src/janus/data/luminosity_tracks/Lum_m1.0.txt | 425 ----------------- src/janus/data/luminosity_tracks/Lum_m1.2.txt | 398 ---------------- src/janus/data/luminosity_tracks/Lum_m1.4.txt | 375 --------------- src/janus/data/tests/data_instellation.csv | 2 +- src/janus/modules/stellar_luminosity.py | 102 ----- tests/test_instellation.py | 21 +- tests/test_runaway_greenhouse.py | 19 +- 13 files changed, 20 insertions(+), 3490 deletions(-) delete mode 100644 src/janus/data/luminosity_tracks/Lum_m0.1.txt delete mode 100644 src/janus/data/luminosity_tracks/Lum_m0.2.txt delete mode 100644 src/janus/data/luminosity_tracks/Lum_m0.4.txt delete mode 100644 src/janus/data/luminosity_tracks/Lum_m0.6.txt delete mode 100644 src/janus/data/luminosity_tracks/Lum_m0.8.txt delete mode 100644 src/janus/data/luminosity_tracks/Lum_m1.0.txt delete mode 100644 src/janus/data/luminosity_tracks/Lum_m1.2.txt delete mode 100644 src/janus/data/luminosity_tracks/Lum_m1.4.txt delete mode 100644 src/janus/modules/stellar_luminosity.py diff --git a/pyproject.toml b/pyproject.toml index 3969d96..286d298 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -37,7 +37,8 @@ dependencies = [ 'seaborn', 'toml', 'tomlkit', - 'f90nml' + 'f90nml', + 'fwl-mors' ] [project.urls] diff --git a/src/janus/data/luminosity_tracks/Lum_m0.1.txt b/src/janus/data/luminosity_tracks/Lum_m0.1.txt deleted file mode 100644 index db3a02d..0000000 --- a/src/janus/data/luminosity_tracks/Lum_m0.1.txt +++ /dev/null @@ -1,433 +0,0 @@ -age,lum 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b/src/janus/data/tests/data_instellation.csv @@ -1,5 +1,5 @@ # r [AU], S_0 [W m-2], OLR [W m-2], net [W m-2], ts [K], tr[K] -3.00000e-01,2.34296e+03,1.94531e+03,-7.41838e+01,3.00037e+03,4.19568e+02 +3.00000e-01,2.34296e+03,1.94531e+03,-7.41821e+01,3.00037e+03,4.19568e+02 4.83333e-01,9.02638e+02,8.44987e+02,6.70043e+01,2.99966e+03,3.30552e+02 6.66667e-01,4.74449e+02,5.02546e+02,9.36275e+01,2.99953e+03,2.81455e+02 8.50000e-01,2.91856e+02,4.21740e+02,1.70194e+02,2.99915e+03,2.49261e+02 diff --git a/src/janus/modules/stellar_luminosity.py b/src/janus/modules/stellar_luminosity.py deleted file mode 100644 index 9678b4d..0000000 --- a/src/janus/modules/stellar_luminosity.py +++ /dev/null @@ -1,102 +0,0 @@ -#!/usr/bin/env python3 -# -*- coding: utf-8 -*- -""" -Created on Mon Jan 23 11:51:59 2023 - -@authors: -Tim Lichtenberg (TL) -Ryan Boukrouche (RB) -Harrison Nicholls (HN) -""" - -import pandas as pd -from scipy import interpolate -import pathlib -import glob, re, os -import numpy as np - -import sys -np.set_printoptions(threshold=sys.maxsize) - -# String sorting not based on natsorted package -def natural_sort(l): - convert = lambda text: int(text) if text.isdigit() else text.lower() - alphanum_key = lambda key: [ convert(c) for c in re.split('([0-9]+)', key) ] - return sorted(l, key = alphanum_key) - -def InterpolateStellarLuminosity(star_mass, time, mean_distance): - - L_sun = 3.828e+26 # W, IAU definition - AU = 1.495978707e+11 # m - - if star_mass >= 0.1 and star_mass <= 1.4: - - # File name - fname = str(pathlib.Path(__file__).parent.parent.absolute())+"/data/luminosity_tracks/Lum_m"+str(star_mass)+".txt" - - # If file exists, just interpolate needed time - if os.path.isfile(fname): - - luminosity_df = pd.read_csv(fname) - star_age = (time["star"])/1e+6 # Myr - ages = luminosity_df["age"]*1e+3 # Myr - luminosities = luminosity_df["lum"] # L_sol - - # Interpolate luminosity for current time - interpolate_luminosity = interpolate.interp1d(ages, luminosities) - interpolated_luminosity = interpolate_luminosity([star_age]) - interpolated_luminosity = interpolated_luminosity[0] - - # Else: interpolate from 2D grid - else: - - # Find all luminosity tracks - lum_tracks = natural_sort(glob.glob(str(pathlib.Path(__file__).parent.parent.absolute())+"/data/luminosity_tracks/"+"Lum_m*.txt")) - # Define data arrays for interpolation later on - xy_age_mass = [] - z_lum = [] - - # Fill the arrays - for lum_track in lum_tracks: - - # Read the specific data file - luminosity_df = pd.read_csv(lum_track) - - # Cut the string to get the mass of the star - star_mass_lst = float(lum_track[-7:-4]) - - # Read out age and luminosity - age_list = list(luminosity_df["age"]*1e+3) - luminosity_list = list(luminosity_df["lum"]) - - mass_list = np.ones(len(age_list))*star_mass_lst - - # Fill the arrays - zip_list = list(zip(age_list, mass_list)) - xy_age_mass.extend(zip_list) - z_lum.extend(luminosity_list) - - # Bring arrays in numpy shape - xy_age_mass = np.array(xy_age_mass) - z_lum = np.array(z_lum) - - # Define the interpolation grids - grid_x, grid_y = np.mgrid[0.7:10000:100j, 0.1:1.4:100j] - - # Interpolate the luminosity from the 2D grid - #print("dimension of xi (time['star']/1e+6, star_mass) = ", np.shape((time["star"]/1e+6, star_mass))) - interpolated_luminosity = interpolate.griddata(xy_age_mass, z_lum, (time["star"]/1e+6, star_mass), method='linear', rescale=True) - print("time['star'] = ", time["star"]) - print("xy_age_mass = ", xy_age_mass) - print("z_lum = ", z_lum) - #print("interpolated_luminosity =", interpolated_luminosity) - - # Stellar luminosity, W m-2 - L_star = interpolated_luminosity * L_sun - - else: # Works only for TRAPPIST-1 right now! - L_star = 0.000553*L_sun # Trappist-1 luminosity - - inst = L_star / ( 4. * np.pi * (mean_distance*AU)**2. ) # Flux at orbital radius (W/m^2) - return inst - diff --git a/tests/test_instellation.py b/tests/test_instellation.py index 7b8de11..986efc4 100755 --- a/tests/test_instellation.py +++ b/tests/test_instellation.py @@ -4,14 +4,9 @@ import os, shutil, toml import numpy as np -from janus.modules.stellar_luminosity import InterpolateStellarLuminosity -from janus.modules.solve_pt import * -from janus.utils.socrates import CleanOutputDir -from janus.utils.atmosphere_column import atmos -import janus.utils.StellarSpectrum as StellarSpectrum -import janus.utils.phys as phys -from janus.utils.ReadSpectralFile import ReadBandEdges -from janus.utils.data import DownloadSpectralFiles +from janus.modules import MCPA_CBL +from janus.utils import atmos, CleanOutputDir, DownloadSpectralFiles, ReadBandEdges, StellarSpectrum +import mors def test_instellation(): @@ -19,7 +14,7 @@ def test_instellation(): if os.environ.get('RAD_DIR') == None: raise Exception("Socrates environment variables not set! Have you installed Socrates and sourced set_rad_env?") 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!") + raise Exception("The FWL_DATA environment variable where spectral and evolution tracks data will be downloaded needs to be set up!") dirs = { "janus": str(files("janus"))+"/", "output": os.path.abspath(os.getcwd())+"/output/" @@ -48,9 +43,11 @@ def test_instellation(): with open(cfg_file, 'r') as f: cfg = toml.load(f) - # Planet + # Star luminosity time = { "planet": cfg['planet']['time'], "star": cfg['star']['time']} star_mass = cfg['star']['star_mass'] + mors.DownloadEvolutionTracks("/Baraffe") + baraffe = mors.BaraffeTrack(star_mass) # Define volatiles by mole fractions vol_mixing = { @@ -65,12 +62,12 @@ def test_instellation(): # Create atmosphere object atm = atmos.from_file(cfg_file, band_edges, vol_mixing=vol_mixing, vol_partial={}) - + r_arr = np.linspace(0.3, 1.4, 7) # orbital distance range [AU] for i in range(7): print("Orbital separation = %.2f AU" % r_arr[i]) - atm.instellation = InterpolateStellarLuminosity(star_mass, time, r_arr[i]) + atm.instellation = baraffe.BaraffeSolarConstant(time['star'], r_arr[i]) atmos.setTropopauseTemperature(atm) atm = MCPA_CBL(dirs, atm, False, rscatter = True, T_surf_max=9.0e99, T_surf_guess = atm.trppT+100) diff --git a/tests/test_runaway_greenhouse.py b/tests/test_runaway_greenhouse.py index 23e8aba..0906a63 100755 --- a/tests/test_runaway_greenhouse.py +++ b/tests/test_runaway_greenhouse.py @@ -5,14 +5,9 @@ from matplotlib.ticker import MultipleLocator from importlib.resources import files -from janus.modules.stellar_luminosity import InterpolateStellarLuminosity -from janus.modules.solve_pt import RadConvEqm -from janus.utils.socrates import CleanOutputDir - -from janus.utils.atmosphere_column import atmos -import janus.utils.StellarSpectrum as StellarSpectrum -from janus.utils.ReadSpectralFile import ReadBandEdges -from janus.utils.data import DownloadSpectralFiles +from janus.modules import RadConvEqm +from janus.utils import atmos, CleanOutputDir, DownloadSpectralFiles, ReadBandEdges, StellarSpectrum +import mors def test_runaway_greenhouse(): @@ -20,7 +15,7 @@ def test_runaway_greenhouse(): if os.environ.get('RAD_DIR') == None: raise Exception("Socrates environment variables not set! Have you installed Socrates and sourced set_rad_env?") 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!") + raise Exception("The FWL_DATA environment variable where spectral and evolution tracks data will be downloaded needs to be set up!") dirs = { "janus": str(files("janus"))+"/", "output": os.path.abspath(os.getcwd())+"/output/" @@ -67,8 +62,10 @@ def test_runaway_greenhouse(): # Create atmosphere object atm = atmos.from_file(cfg_file, band_edges, vol_mixing=vol_mixing, vol_partial={}) - # Compute stellar heating - atm.instellation = InterpolateStellarLuminosity(star_mass, time, mean_distance) + # Compute stellar heating from Baraffe evolution tracks + mors.DownloadEvolutionTracks("/Baraffe") + baraffe = mors.BaraffeTrack(star_mass) + atm.instellation = baraffe.BaraffeSolarConstant(time['star'], mean_distance) #Run Janus Ts_arr = np.linspace(200, 2800, 20)