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Merge pull request #49 from FormingWorlds/outspec
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Writes output files in a consistent format
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@nichollsh
nichollsh authored Aug 7, 2024
2 parents 97ab299 + 6930096 commit fc4786b
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Showing 3 changed files with 46 additions and 36 deletions.
2 changes: 1 addition & 1 deletion examples/SocRadConv.py
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Original file line number Diff line number Diff line change
Expand Up @@ -69,7 +69,7 @@
os.mkdir(dirs["output"])

#Download required spectral files
DownloadSpectralFiles("/Dayspring")
DownloadSpectralFiles("Dayspring")
DownloadStellarSpectra()

# Read spectrum
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3 changes: 2 additions & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,8 @@ dependencies = [
'toml',
'tomlkit',
'f90nml',
'fwl-mors'
'fwl-mors',
'datetime'
]

[project.urls]
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77 changes: 43 additions & 34 deletions src/janus/utils/atmosphere_column.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@
from janus.utils.height import AtmosphericHeight
import os, copy, platform, shutil
import pwd
from datetime import datetime

class atmos:

Expand Down Expand Up @@ -356,6 +357,11 @@ def write_ncdf(self, fpath:str):
Output filename
"""

# Get SOCRATES version string
verpath = os.path.join(os.environ.get("RAD_DIR"),"version")
with open(verpath, 'r') as hdl:
SOCRATES_version = hdl.read().replace("\n","")

# ----------------------
# Calculate gravity and height (in case it hasn't been done already)
self.z = AtmosphericHeight(self, self.planet_mass, self.planet_radius)
Expand All @@ -371,19 +377,24 @@ def write_ncdf(self, fpath:str):
os.remove(fpath)

ds = nc.Dataset(fpath, 'w', format='NETCDF4')
ds.description = 'JANUS atmosphere data'
ds.hostname = str(platform.node())

# Metadata
try:
# Try to get the login using os.getlogin()
username = os.getlogin()
except OSError:
# If os.getlogin() fails, try an alternative method
username = pwd.getpwuid(os.getuid()).pw_name
ds.username = str(username)
ds.JANUS_version = "0.1"
ds.SOCRATES_version = "2306"
ds.platform = str(platform.system())
ds.username = str(username)
ds.JANUS_version = "0.1"
ds.SOCRATES_version = str(SOCRATES_version)
ds.platform = str(platform.system())
ds.date = str(datetime.now().strftime('%Y-%m-%d %H:%M:%S'))
ds.description = 'JANUS atmosphere data'
ds.hostname = str(platform.node())

# ----------------------
# Variable sizes
nlev_c = len(self.p)
nlev_l = nlev_c + 1

Expand All @@ -392,21 +403,18 @@ def write_ncdf(self, fpath:str):

nchars = 16

# ----------------------
# Create dimensions
ds.createDimension('nlev_c', nlev_c) # Cell centres
ds.createDimension('nlev_l', nlev_l) # Cell edges
ds.createDimension('ngases', ngases) # Gases
ds.createDimension('nchars', nchars) # Length of string containing gas names
ds.createDimension('nbands', self.nbands) # Number of bands in the spectral file
ds.createDimension('nedges', self.nbands+1)
ds.createDimension('nlev_c', nlev_c) # Cell centres
ds.createDimension('nlev_l', nlev_l) # Cell edges
ds.createDimension('ngases', ngases) # Gases
ds.createDimension('nchars', nchars) # Length of string containing gas names
ds.createDimension('nbands', self.nbands) # Number of bands in the spectral file
ds.createDimension('nchannels', self.nbands)

# ----------------------
# Scalar quantities
# Create variables
var_tstar = ds.createVariable('tstar', 'f4'); var_tstar.units = "K" # BOA LW BC
var_ps = ds.createVariable('ps', 'f4'); var_ps.units = "Pa"
var_ptop = ds.createVariable('ptop', 'f4'); var_ptop.units = "Pa"
var_tstar = ds.createVariable('tmp_surf', 'f4'); var_tstar.units = "K" # Ground temperature
var_trppP = ds.createVariable('trppP', 'f4'); var_trppP.units = "Pa"
var_inst = ds.createVariable("instellation", 'f4'); var_inst.units = "W m-2" # Solar flux at TOA
var_s0fact = ds.createVariable("inst_factor", 'f4'); # Scale factor applied to instellation
Expand All @@ -426,8 +434,6 @@ def write_ncdf(self, fpath:str):
var_tstar.assignValue(self.ts)
var_inst.assignValue(self.instellation)
var_toah.assignValue(self.toa_heating)
var_ps.assignValue(self.ps)
var_ptop.assignValue(self.ptop)
var_trppP.assignValue(self.trppP)
var_znth.assignValue(self.zenith_angle)
var_s0fact.assignValue(self.inst_sf)
Expand All @@ -453,8 +459,6 @@ def write_ncdf(self, fpath:str):
var_zl = ds.createVariable('zl', 'f4', dimensions=('nlev_l')); var_zl.units = "m"
var_grav = ds.createVariable('gravity', 'f4', dimensions=('nlev_c')); var_grav.units = "m s-2"
var_cp = ds.createVariable('cp', 'f4', dimensions=('nlev_c')); var_cp.units = "J/(kg K)"
var_xd = ds.createVariable('xd', 'f4', dimensions=('nlev_c')); var_xd.units = "none"
var_xv = ds.createVariable('xv', 'f4', dimensions=('nlev_c')); var_xv.units = "none"

var_mmw = ds.createVariable('mmw', 'f4', dimensions=('nlev_c')); var_mmw.units = "kg mol-1"
var_gases = ds.createVariable('gases', 'S1', dimensions=('ngases', 'nchars')) # Names of gases
Expand All @@ -472,15 +476,18 @@ def write_ncdf(self, fpath:str):
var_fd = ds.createVariable('fl_D', 'f4', dimensions=('nlev_l')); var_fd.units = "W m-2"
var_fu = ds.createVariable('fl_U', 'f4', dimensions=('nlev_l')); var_fu.units = "W m-2"
var_fn = ds.createVariable('fl_N', 'f4', dimensions=('nlev_l')); var_fn.units = "W m-2"
var_hr = ds.createVariable('rad_hr', 'f4', dimensions=('nlev_c')); var_hr.units = "K day-1"
var_sful = ds.createVariable('Sfl_U_LW','f4', dimensions=('nbands', 'nlev_l')); var_sful.units = "W m-2"
var_sfus = ds.createVariable('Sfl_U_SW','f4', dimensions=('nbands', 'nlev_l')); var_sfus.units = "W m-2"
var_sfdl = ds.createVariable('Sfl_D_LW','f4', dimensions=('nbands', 'nlev_l')); var_sfdl.units = "W m-2"
var_sfds = ds.createVariable('Sfl_D_SW','f4', dimensions=('nbands', 'nlev_l')); var_sfds.units = "W m-2"
var_edge = ds.createVariable('band_edges','f4', dimensions=('nedges')); var_edge.units = "nm"
var_hr = ds.createVariable('hrate', 'f4', dimensions=('nlev_c')); var_hr.units = "K day-1"
var_bul = ds.createVariable('ba_U_LW','f4', dimensions=('nbands', 'nlev_l')); var_bul.units = "W m-2"
var_bdl = ds.createVariable('ba_D_LW','f4', dimensions=('nbands', 'nlev_l')); var_bdl.units = "W m-2"
var_bnl = ds.createVariable('ba_N_LW','f4', dimensions=('nbands', 'nlev_l')); var_bnl.units = "W m-2"
var_bus = ds.createVariable('ba_U_SW','f4', dimensions=('nbands', 'nlev_l')); var_bus.units = "W m-2"
var_bds = ds.createVariable('ba_D_SW','f4', dimensions=('nbands', 'nlev_l')); var_bds.units = "W m-2"
var_bns = ds.createVariable('ba_N_SW','f4', dimensions=('nbands', 'nlev_l')); var_bns.units = "W m-2"
var_bmin = ds.createVariable('bandmin','f4', dimensions=('nbands')); var_bmin.units = "m"
var_bmax = ds.createVariable('bandmax','f4', dimensions=('nbands')); var_bmax.units = "m"

if self.has_contfunc:
var_cff = ds.createVariable('cff', 'f4', dimensions=('nbands', 'nlev_c')); var_cff.units = "W m-2 m-1" ## units??
var_cff = ds.createVariable('contfunc', 'f4', dimensions=('nbands', 'nlev_c')); var_cff.units = "W m-2 m-1" ## units??

var_re = ds.createVariable('re', 'f4', dimensions=('nlev_c')); var_re.units = "m"
var_lwm = ds.createVariable('lwm', 'f4', dimensions=('nlev_c')); var_lwm.units = "kg kg-1"
Expand All @@ -496,8 +503,6 @@ def write_ncdf(self, fpath:str):
var_mmw[:] = self.mu[:]
var_grav[:] = self.grav_z[:]
var_cp[:] = self.cp[:]
var_xd[:] = self.xd[:]
var_xv[:] = self.xv[:]

var_gases[:] = np.array([ [c for c in gas.ljust(nchars)[:nchars]] for gas in gas_list ] , dtype='S1')
var_mr[:] = np.array([ [ self.x_gas[gas][i] for i in range(nlev_c-1,-1,-1) ] for gas in gas_list ]).T
Expand All @@ -520,12 +525,16 @@ def write_ncdf(self, fpath:str):

var_hr[:] = self.net_heating[:]

var_sful[:,:] = self.LW_spectral_flux_up[:,:]
var_sfus[:,:] = self.SW_spectral_flux_up[:,:]
var_sfdl[:,:] = self.LW_spectral_flux_down[:,:]
var_sfds[:,:] = self.SW_spectral_flux_down[:,:]
var_bul[:,:] = self.LW_spectral_flux_up[:,:]
var_bdl[:,:] = self.LW_spectral_flux_down[:,:]
var_bnl[:,:] = var_bul[:,:] - var_bdl[:,:]

var_bus[:,:] = self.SW_spectral_flux_up[:,:]
var_bds[:,:] = self.SW_spectral_flux_down[:,:]
var_bns[:,:] = var_bus[:,:] - var_bds[:,:]

var_edge[:] = self.band_edges[:]
var_bmin[:] = self.band_edges[:-1] * 1e-9
var_bmax[:] = self.band_edges[1:] * 1e-9

if self.has_contfunc:
var_cff[:,:] = self.cff[:,:]
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