Merge pull request #34 from FormingWorlds/fixes

Minor fixes and download stellar spectrum

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.   
 
@@ -36,12 +36,13 @@ https://proteus-code.readthedocs.io
     * `git clone [email protected]:FormingWorlds/JANUS.git`
     * `cd JANUS`
     * `pip install -e .`
-3. Download spectral files from the [OSF repository](https://osf.io/vehxg/)
+3. Download data from the [OSF repository](https://osf.io/vehxg/)
     * Set the environment variable FWL_DATA to define where the spectral data files will be stored
         * `export FWL_DATA=...`
-    * Run the following commands within a python environment (or script) to download all basic spectral files
-        * `from janus.utils.data import DownloadSpectralFiles`
+    * Run the following commands within a python environment (or script) to download all basic data
+        * `from janus.utils.data import *`
         * `DownloadSpectralFiles()`
+        * `DownloadStellarSpectra()`
     * Alternatively, you can specify which spectral data you want to download, and optionally the number of bands
     * `DownloadSpectralFiles("/Frostflow", 4096)`
 

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
 
 ####################################
@@ -70,13 +70,21 @@
 
     #Download required spectral files
     DownloadSpectralFiles("/Dayspring")
-    DownloadSpectralFiles("/stellar_spectra")
+    DownloadStellarSpectra()
+
+    # Read spectrum
+    spec = mors.Spectrum()
+    spec.LoadTSV(os.environ.get('FWL_DATA')+"/stellar_spectra/Named/sun.txt")
+
+    # Convert to SOCRATES format 
+    socstar = os.path.join(dirs["output"], "socstar.txt")
+    StellarSpectrum.PrepareStellarSpectrum(spec.wl, spec.fl, socstar)
 
     # Move/prepare spectral file
     print("Inserting stellar spectrum")
     StellarSpectrum.InsertStellarSpectrum(
         os.environ.get('FWL_DATA')+"/spectral_files/Dayspring/256/Dayspring.sf",
-        os.environ.get('FWL_DATA')+"/spectral_files/stellar_spectra/Sun_t4_4Ga_claire_12.txt",
+        socstar,
         dirs["output"]
     )
 

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
 
@@ -37,13 +37,22 @@
 
     #Download required spectral files
     DownloadSpectralFiles("/Oak")
-    DownloadSpectralFiles("/stellar_spectra")
+    DownloadStellarSpectra()
+
+    # Read spectrum
+    spec = mors.Spectrum()
+    spec.LoadTSV(os.environ.get('FWL_DATA')+"/stellar_spectra/Named/sun.txt")
+
+    # Convert to SOCRATES format 
+    socstar = os.path.join(dirs["output"], "socstar.txt")
+    StellarSpectrum.PrepareStellarSpectrum(spec.wl, spec.fl, socstar)
+
 
     # Setup spectral file
     print("Inserting stellar spectrum")
     StellarSpectrum.InsertStellarSpectrum(
         os.environ.get('FWL_DATA')+"/spectral_files/Oak/318/Oak.sf",
-        os.environ.get('FWL_DATA')+"/spectral_files/stellar_spectra/Sun_t4_4Ga_claire_12.txt",
+        socstar,
         dirs["output"]
     )
     band_edges = ReadBandEdges(dirs["output"]+"star.sf")

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__':
@@ -36,13 +36,22 @@
 
     #Download required spectral files
     DownloadSpectralFiles("/Oak")
-    DownloadSpectralFiles("/stellar_spectra")
+    DownloadStellarSpectra()
+
+    # Read spectrum
+    spec = mors.Spectrum()
+    spec.LoadTSV(os.environ.get('FWL_DATA')+"/stellar_spectra/Named/sun.txt")
+
+    # Convert to SOCRATES format 
+    socstar = os.path.join(dirs["output"], "socstar.txt")
+    StellarSpectrum.PrepareStellarSpectrum(spec.wl, spec.fl, socstar)
+
 
     # Setup spectral file
     print("Inserting stellar spectrum")
     StellarSpectrum.InsertStellarSpectrum(
         os.environ.get('FWL_DATA')+"/spectral_files/Oak/318/Oak.sf",
-        os.environ.get('FWL_DATA')+"/spectral_files/stellar_spectra/Sun_t4_4Ga_claire_12.txt",
+        socstar,
         dirs["output"]
     )
     print(" ")

src/janus/data/tests/data_instellation.csv

@@ -1,8 +1,8 @@
 # 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,-7.41821e+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
-1.03333e+00,1.97481e+02,4.17035e+02,2.46829e+02,2.99877e+03,2.26070e+02
-1.21667e+00,1.42450e+02,4.16624e+02,2.93848e+02,2.99853e+03,2.08342e+02
-1.40000e+00,1.07585e+02,4.16473e+02,3.23747e+02,2.99838e+03,1.94222e+02
+3.00000e-01,2.34297e+03,1.94397e+03,-4.67185e+01,3.00023e+03,4.19568e+02
+4.83333e-01,9.02641e+02,8.43916e+02,7.70272e+01,2.99961e+03,3.30552e+02
+6.66667e-01,4.74451e+02,5.01731e+02,9.86425e+01,2.99951e+03,2.81454e+02
+8.50000e-01,2.91857e+02,4.21028e+02,1.73069e+02,2.99913e+03,2.49260e+02
+1.03333e+00,1.97482e+02,4.16319e+02,2.48540e+02,2.99876e+03,2.26070e+02
+1.21667e+00,1.42451e+02,4.15915e+02,2.94890e+02,2.99853e+03,2.08342e+02
+1.40000e+00,1.07585e+02,4.15768e+02,3.24365e+02,2.99838e+03,1.94222e+02

src/janus/data/tests/data_runaway_greenhouse.csv

@@ -1,21 +1,21 @@
 # T_surf [K], OLR [W m-2]
- 200.00000000,   90.72589
- 336.84210526,  277.55026
- 473.68421053,  277.47986
- 610.52631579,  277.27164
- 747.36842105,  277.35020
- 884.21052632,  277.18277
-1021.05263158,  277.37436
-1157.89473684,  277.13092
-1294.73684211,  277.14750
-1431.57894737,  277.30030
-1568.42105263,  277.64148
-1705.26315789,  279.04703
-1842.10526316,  285.55804
-1978.94736842,  308.2808
-2115.78947368,  375.7102
-2252.63157895,  548.4764
-2389.47368421,  954.2722
-2526.31578947, 1821.3682
-2663.15789474, 3517.7295 
-2800.00000000, 6636.2110 
+ 200.00000000,9.07314e+01 
+ 336.84210526,2.77416e+02 
+ 473.68421053,2.77349e+02 
+ 610.52631579,2.77138e+02
+ 747.36842105,2.77217e+02
+ 884.21052632,2.77049e+02
+1021.05263158,2.77241e+02
+1157.89473684,2.76997e+02
+1294.73684211,2.77013e+02
+1431.57894737,2.77166e+02
+1568.42105263,2.77504e+02
+1705.26315789,2.78884e+02
+1842.10526316,2.85329e+02
+1978.94736842,3.07788e+02
+2115.78947368,3.74184e+02
+2252.63157895,5.47014e+02
+2389.47368421,9.50390e+02
+2526.31578947,1.80287e+03
+2663.15789474,3.49537e+03
+2800.00000000,6.58174e+03

src/janus/modules/plot_emission_spectrum.py

@@ -7,7 +7,8 @@
 import janus.utils.phys as phys
 
 def plot_emission(atm:atmos, filename:str='output/toa_emission.pdf', 
-                  level_idx:int=0, planck_surface:bool=True, show_bands:bool=False):
+                  level_idx:int=0, planck_surface:bool=True, 
+                  incoming_solar:bool=True, show_bands:bool=False):
 
     # Configure
     planck_samps = 1000
@@ -34,6 +35,13 @@ def plot_emission(atm:atmos, filename:str='output/toa_emission.pdf',
     # Make plot 
     fig,ax = plt.subplots(1,1, figsize=(8,4))
 
+    # Plot incoming stellar spectrum
+    if incoming_solar:
+        ysolar = atm.SW_spectral_flux_down.T[0] # W m-2 
+        ysolar /= atm.band_widths 
+        ysolar *= 1e3 
+        ax.plot(x, ysolar, color="green", lw=lw, label="TOA stellar flux")
+
     # Plot band edges
     if show_bands:
         for i in range(atm.nbands):
@@ -70,7 +78,7 @@ def plot_emission(atm:atmos, filename:str='output/toa_emission.pdf',
     ax.set_xlim(max(xmin, np.amin(x)), min(xmax, np.amax(x)))
     ax.set_xscale("log")
 
-    ax.set_ylabel("Upward flux [erg s$^{-1}$ cm$^{-2}$ nm$^{-1}$]")
+    ax.set_ylabel("Flux density [erg s$^{-1}$ cm$^{-2}$ nm$^{-1}$]")
     ax.set_yscale("log")
 
     ax.legend(loc="lower center")