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build_atm.py
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build_atm.py
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import numpy as np
from numpy import polynomial
import scipy
from scipy import interpolate
import scipy.optimize as sop
import subprocess
import pickle
from shutil import copyfile
import vulcan_cfg
from phy_const import kb, Navo, r_sun, au
from vulcan_cfg import nz
import chem_funs
from chem_funs import ni, nr # number of species and reactions in the network
species = chem_funs.spec_list
### read in the basic chemistry data
with open(vulcan_cfg.com_file, 'r') as f:
columns = f.readline() # reading in the first line
num_ele = len(columns.split())-2 # number of elements (-2 for removing "species" and "mass")
type_list = ['int' for i in range(num_ele)]
type_list.insert(0,'U20'); type_list.append('float')
compo = np.genfromtxt(vulcan_cfg.com_file,names=True,dtype=type_list)
# dtype=None in python 2.X but Sx -> Ux in python3
compo_row = list(compo['species'])
### read in the basic chemistry data
class InitialAbun(object):
"""
Calculating the appropriate initial mixing ratios with the assigned elemental abundance
"""
def __init__(self):
self.ini_m = [0.9,0.1,0.,0.,0] # initial guess
#self.EQ_ini_file = vulcan_cfg.EQ_ini_file
self.atom_list = vulcan_cfg.atom_list
def abun_lowT(self, x):
"""
calculating the initial mixing ratios of the following 5 molecules (with CH4)
satisfying the assigned elemental abundance
x1:H2 x2:H2O x3:CH4 x4:He x5:NH3
"""
O_H, C_H, He_H, N_H = vulcan_cfg.O_H, vulcan_cfg.C_H, vulcan_cfg.He_H, vulcan_cfg.N_H
x1,x2,x3,x4,x5 = x
f1 = x1+x2+x3+x4-1.
f2 = x2 - (2*x1+2*x2+4*x3+3*x5)*O_H
f3 = x3 - (2*x1+2*x2+4*x3+3*x5)*C_H
f4 = x4 - (2*x1+2*x2+4*x3+3*x5)*He_H
f5 = x5 - (2*x1+2*x2+4*x3+3*x5)*N_H
return f1,f2,f3,f4,f5
def abun_highT(self, x):
"""
calculating the initial mixing ratios of the following 4 molecules (with CO)
satisfying the assigned elemental abundance
x1:H2 x2:H2O x3:CO x4:He x5:N2
"""
O_H, C_H, He_H, N_H = vulcan_cfg.O_H, vulcan_cfg.C_H, vulcan_cfg.He_H, vulcan_cfg.N_H
x1,x2,x3,x4,x5 = x
f1 = x1+x2+x3+x4-1.
f2 = x2+x3 - (2*x1+2*x2)*O_H
f3 = x3 - (2*x1+2*x2)*C_H
f4 = x4 - (2*x1+2*x2)*He_H
f5 = x5*2 - (2*x1+2*x2)*N_H
return f1,f2,f3,f4,f5
def ini_mol(self):
if vulcan_cfg.ini_mix == 'const_lowT':
return np.array(sop.fsolve(self.abun_lowT, self.ini_m))
# somehow const_highT is not stable at high P...
# elif vulcan_cfg.ini_mix == 'const_highT':
# return np.array(sop.fsolve(self.abun_highT, self.ini_m))
def ini_fc(self, data_var, data_atm):
# reading-in the default elemental abundances from Lodders 2009
# depending on including ion or not (whether there is e- in the fastchem elemental abundance dat)
tmp_str = ""
solar_ele = 'fastchem_vulcan/input/solar_element_abundances.dat'
if vulcan_cfg.use_ion == True:
copyfile('fastchem_vulcan/input/parameters_ion.dat', 'fastchem_vulcan/input/parameters.dat')
else:
copyfile('fastchem_vulcan/input/parameters_wo_ion.dat', 'fastchem_vulcan/input/parameters.dat')
with open(solar_ele ,'r') as f:
new_str = ""
ele_list = list(vulcan_cfg.atom_list)
ele_list.remove('H')
fc_list = ['C', 'N', 'O', 'S', 'P', 'Si', 'Ti','V','Cl','K','Na','Mg','F','Ca','Fe']
if vulcan_cfg.use_solar == True:
new_str = f.read() # read in as a string
print ("Initializing with the default solar abundance.")
else: # using costomized elemental abundances
print ("Initializing with the customized elemental abundance:")
print ("{:4}".format('H') + str('1.'))
for line in f.readlines():
li = line.split()
sp = li[0].strip()
if sp in ele_list:
# read-in vulcan_cfg.sp_H
sp_abun = getattr(vulcan_cfg, sp+'_H')
fc_abun = 12. + np.log10(sp_abun)
line = sp + '\t' + "{0:.4f}".format(fc_abun) + '\n'
print ("{:4}".format(sp) + "{0:.4E}".format(sp_abun))
elif sp in fc_list: # other elements included in fastchem but not in VULCAN
sol_ratio = li[1].strip()
# print (sp + ": " + str(sol_ratio))
if hasattr(vulcan_cfg, 'fastchem_met_scale'): # vulcan_cfg.fastchem_met_scale exists
met_scale = vulcan_cfg.fastchem_met_scale
else:
met_scale = 1.
print ("fastchem_met_scale not specified in vulcan_cfg. Using solar metallicity for other elements not included in vulcan.")
new_ratio = float(sol_ratio) + np.log10(met_scale)
line = sp + '\t' + "{0:.4f}".format(new_ratio) + '\n'
new_str += line
# make the new elemental abundance file
with open('fastchem_vulcan/input/element_abundances_vulcan.dat', 'w') as f: f.write(new_str)
# write a T-P text file for fast_chem
with open('fastchem_vulcan/input/vulcan_TP/vulcan_TP.dat' ,'w') as f:
ost = '#p (bar) T (K)\n'
for n, p in enumerate(data_atm.pco): # p in bar in fast_chem
ost += '{:.3e}'.format(p/1.e6) + '\t' + '{:.1f}'.format(data_atm.Tco[n]) + '\n'
ost = ost[:-1]
f.write(ost)
try: subprocess.check_call(["./fastchem input/config.input"], shell=True, cwd='fastchem_vulcan/') # check_call instead of call can catch the error
except: print ('\n FastChem cannot run properly. Try compile it by running make under /fastchem_vulcan\n'); raise
def ini_y(self, data_var, data_atm):
# initial mixing ratios of the molecules
ini_mol = self.ini_mol()
ini = np.zeros(ni)
y_ini = data_var.y
gas_tot = data_atm.M
charge_list = [] # list of charged species excluding echarge_list
if vulcan_cfg.ini_mix == 'EQ':
self.ini_fc(data_var, data_atm)
fc = np.genfromtxt('fastchem_vulcan/output/vulcan_EQ.dat', names=True, dtype=None, skip_header=0)
for sp in species:
if sp in fc.dtype.names:
y_ini[:,species.index(sp)] = fc[sp]*gas_tot # this also changes data_var.y because the address of y array has passed to y_ini
else: print (sp + ' not included in fastchem.')
if vulcan_cfg.use_ion == True:
if compo[compo_row.index(sp)]['e'] != 0: charge_list.append(sp)
# remove the fc output
subprocess.call(["rm vulcan_EQ.dat"], shell=True, cwd='fastchem_vulcan/output/')
elif vulcan_cfg.ini_mix == 'vulcan_ini':
print ("Initializing with compositions from the prvious run " + vulcan_cfg.vul_ini)
with open(vulcan_cfg.vul_ini, 'rb') as handle:
vul_data = pickle.load(handle)
#y_ini = np.copy(vul_data['variable']['y'])
#data_var.y = np.copy(y_ini)
for sp in species:
if sp in vul_data['variable']['species']:
y_ini[:,species.index(sp)] = vul_data['variable']['y'][:,vul_data['variable']['species'].index(sp)]
else: print (sp + " not included in the prvious run.")
#if vulcan_cfg.use_ion == True: charge_list = vul_data['variable']['charge_list']
if vulcan_cfg.use_ion == True:
for sp in species:
if compo[compo_row.index(sp)]['e'] != 0: charge_list.append(sp)
elif vulcan_cfg.ini_mix == 'table':
table = np.genfromtxt(vulcan_cfg.vul_ini, names=True, dtype=None, skip_header=1)
if not len(data_atm.pco) == len(table['Pressure']):
print ("Warning! The initial profile has different layers than the current setting...")
raise
for sp in species:
data_var.y[:,species.index(sp)] = data_atm.n_0 * table[sp]
elif vulcan_cfg.ini_mix == 'const_mix':
print ("Initializing with constant (well-mixed): " + str(vulcan_cfg.const_mix))
for sp in vulcan_cfg.const_mix.keys():
y_ini[:,species.index(sp)] = gas_tot* vulcan_cfg.const_mix[sp] # this also changes data_var.y
if vulcan_cfg.use_ion == True:
for sp in species:
if compo[compo_row.index(sp)]['e'] != 0: charge_list.append(sp)
else:
for i in range(nz):
if vulcan_cfg.ini_mix == 'const_lowT':
y_ini[i,:] = ini
y_ini[i,species.index('H2')] = ini_mol[0]*gas_tot[i]; y_ini[i,species.index('H2O')] = ini_mol[1]*gas_tot[i]; y_ini[i,species.index('CH4')] = ini_mol[2]*gas_tot[i]
y_ini[i,species.index('NH3')] = ini_mol[4]*gas_tot[i]
# assign rest of the particles to He
y_ini[i,species.index('He')] = gas_tot[i] - np.sum(y_ini[i,:])
else:
raise IOError ('\nInitial mixing ratios unknown. Check the setting in vulcan_cfg.py.')
if vulcan_cfg.use_condense == True:
for sp in vulcan_cfg.condense_sp:
data_atm.sat_mix[sp] = data_atm.sat_p[sp]/data_atm.pco
# fixed 2022
data_atm.sat_mix[sp] = np.minimum(1., data_atm.sat_mix[sp])
if sp == 'H2O': data_atm.sat_mix[sp] *= vulcan_cfg.humidity
if vulcan_cfg.use_ini_cold_trap == True:
if vulcan_cfg.ini_mix != 'table' and vulcan_cfg.ini_mix != 'vul_ini':
# the level where condensation starts
conden_bot = np.argmax( data_atm.n_0*data_atm.sat_mix[sp] <= data_var.y[:,species.index(sp)] )
# conden_status: ture if the partial p >= the saturation p
sat_rho = data_atm.n_0 * data_atm.sat_mix[sp]
conden_status = data_var.y[:,species.index(sp)] >= sat_rho
# take the min between the mixing ratio and the saturation mixing ratio
data_var.y[:,species.index(sp)] = np.minimum(data_atm.n_0 * data_atm.sat_mix[sp], data_var.y[:,species.index(sp)])
if list(data_var.y[conden_status,species.index(sp)]): # if it condenses
min_sat = np.amin(data_atm.sat_mix[sp][conden_status]) # the mininum value of the saturation p within the saturation region
conden_min_lev = np.where(data_atm.sat_mix[sp] == min_sat)[0][0]
data_atm.conden_min_lev = conden_min_lev
print ( sp + " condensed from nz = " + str(conden_bot) + " to the minimum level nz = "+ str(conden_min_lev) + " (cold trap)")
#data_var.y[conden_min_lev:,species.index(sp)] = (y_ini[conden_min_lev,species.index(sp)]/data_atm.n_0[conden_min_lev]) *data_atm.n_0[conden_min_lev:]
data_var.y[conden_min_lev:,species.index(sp)] = data_atm.sat_mix[sp][conden_min_lev] * data_atm.n_0[conden_min_lev:]
# re-normalisation
# TEST
# Excluding the non-gaseous species
if vulcan_cfg.use_condense == True:
exc_conden = [_ for _ in range(ni) if species[_] not in vulcan_cfg.non_gas_sp]
ysum = np.sum(y_ini[:,exc_conden], axis=1).reshape((-1,1))
else:
ysum = np.sum(y_ini, axis=1).reshape((-1,1))
data_var.y_ini = np.copy(y_ini)
data_var.ymix = y_ini/ysum
if vulcan_cfg.use_ion == True:
# if the charge_list is empty (no species with nonzero charges include)
if not charge_list:
print ( "vulcan_cfg.use_ion = True but the network with ions is not supplied.\n" )
raise IOError("vulcan_cfg.use_ion = True but the network with ions is not supplied.\n")
else:
if 'e' in charge_list: charge_list.remove('e')
data_var.charge_list = charge_list
return data_var
def ele_sum(self, data_var):
for atom in self.atom_list:
data_var.atom_ini[atom] = np.sum([compo[compo_row.index(species[i])][atom] * data_var.y[:,i] for i in range(ni)])
data_var.atom_loss[atom] = 0.
data_var.atom_conden[atom] = 0.
return data_var
class Atm(object):
def __init__(self):
self.gs = vulcan_cfg.gs # gravity
self.P_b = vulcan_cfg.P_b
self.P_t = vulcan_cfg.P_t
self.type = vulcan_cfg.atm_type
self.use_Kzz = vulcan_cfg.use_Kzz
self.Kzz_prof = vulcan_cfg.Kzz_prof
self.const_Kzz = vulcan_cfg.const_Kzz
self.use_vz = vulcan_cfg.use_vz
self.vz_prof = vulcan_cfg.vz_prof
self.const_vz = vulcan_cfg.const_vz
self.use_settling = vulcan_cfg.use_settling
self.non_gas_sp = vulcan_cfg.non_gas_sp
def f_pico(self, data_atm):
'''calculating the pressure at interface'''
pco = data_atm.pco
# construct pico
pco_up1 = np.roll(pco,1)
pi = (pco * pco_up1)**0.5
pi[0] = pco[0]**1.5 * pco[1]**(-0.5)
pi = np.append(pi,pco[-1]**1.5 * pco[-2]**(-0.5))
# store pico
data_atm.pico = pi
#data_atm.pco = pco
return data_atm
def load_TPK(self, data_atm):
PTK_fun = {}
# IF switches for TP types
if self.type == 'isothermal':
data_atm.Tco = np.repeat(vulcan_cfg.Tiso,nz)
#data_atm.Kzz = np.repeat(self.const_Kzz,nz-1)
#data_atm.vz = np.repeat(self.const_vz,nz-1)
elif self.type == 'analytical':
# plotting T-P on the fly
para_atm = vulcan_cfg.para_anaTP
# return the P-T function
PTK_fun['pT'] = lambda pressure: self.TP_H14(pressure, *para_atm)
data_atm.Tco = PTK_fun['pT'](data_atm.pco)
#data_atm.Kzz = np.repeat(self.const_Kzz,nz-1)
#data_atm.vz = np.repeat(self.const_vz,nz-1)
# for atm_type = 'file' and also Kzz_prof = 'file
elif self.type == 'file':
if self.Kzz_prof == 'file':
atm_table = np.genfromtxt(vulcan_cfg.atm_file, names=True, dtype=None, skip_header=1)
p_file, T_file, Kzz_file = atm_table['Pressure'], atm_table['Temp'], atm_table['Kzz']
else:
atm_table = np.genfromtxt(vulcan_cfg.atm_file, names=True, dtype=None, skip_header=1)
p_file, T_file = atm_table['Pressure'], atm_table['Temp']
if max(p_file) < data_atm.pco[0] or min(p_file) > data_atm.pco[-1]:
print ('Warning: P_b and P_t assgined in vulcan.cfg are out of range of the input.\nConstant extension is used.')
PTK_fun['pT'] = interpolate.interp1d(p_file, T_file, assume_sorted = False, bounds_error=False,\
fill_value=(T_file[np.argmin(p_file)], T_file[np.argmax(p_file)] ) )
# store Tco in data_atm
try:
data_atm.Tco = PTK_fun['pT'](data_atm.pco)
# for SciPy earlier than v0.18.0
except ValueError:
PTK_fun['pT'] = interpolate.interp1d(p_file, T_file, assume_sorted = False, bounds_error=False, fill_value=T_file[np.argmin(p_file)] )
data_atm.Tco = PTK_fun['pT'](data_atm.pco)
if self.use_Kzz == True and self.Kzz_prof == 'file':
PTK_fun['pK'] = interpolate.interp1d(p_file, Kzz_file, assume_sorted = False, bounds_error=False, fill_value=(Kzz_file[np.argmin(p_file)], Kzz_file[np.argmax(p_file)]) )
# store Kzz in data_atm
try:
data_atm.Kzz = PTK_fun['pK'](data_atm.pico[1:-1])
# for SciPy earlier than v0.18.0
except ValueError:
PTK_fun['pK'] = interpolate.interp1d(p_file, Kzz_file, assume_sorted = False, bounds_error=False, fill_value=Kzz_file[np.argmin(p_file)] )
data_atm.Kzz = PTK_fun['pK'](data_atm.pico[1:-1])
elif self.Kzz_prof == 'const': data_atm.Kzz = np.repeat(self.const_Kzz,nz-1)
elif self.type == 'vulcan_ini':
print ("Initializing PT from the prvious run " + vulcan_cfg.vul_ini)
with open(vulcan_cfg.vul_ini, 'rb') as handle:
vul_data = pickle.load(handle)
data_atm.Tco = vul_data['atm']['Tco']
elif self.type == 'table':
print ("Initializing PT from the prvious run " + vulcan_cfg.vul_ini)
table = np.genfromtxt(vulcan_cfg.vul_ini, names=True, dtype=None, skip_header=1)
if not len(data_atm.pco) == len(table['Pressure']):
print ("Warning! The initial profile has different layers than the current setting...")
raise
data_atm.pco = table['Pressure']
data_atm.Tco = table['Temp']
else: raise IOError ('\n"atm_type" cannot be recongized.\nPlease trassign it in vulcan_cfg.')
# IF switches for Kzz types
if self.Kzz_prof == 'const': data_atm.Kzz = np.repeat(self.const_Kzz,nz-1)
elif self.Kzz_prof == 'JM16': # Kzz profiles assumed in Moses et al.2016
data_atm.Kzz = 1e5 * (300./(data_atm.pico[1:-1]*1e-3))**0.5
data_atm.Kzz = np.maximum(vulcan_cfg.K_deep, data_atm.Kzz)
elif self.Kzz_prof == 'Pfunc': # Kzz profiles assumed in Tsai 2020
data_atm.Kzz = vulcan_cfg.K_max * (vulcan_cfg.K_p_lev*1e6 /(data_atm.pico[1:-1]))**0.4
data_atm.Kzz = np.maximum(vulcan_cfg.K_max, data_atm.Kzz)
elif self.Kzz_prof == 'file': pass # already defined within atm_type = 'file
else: raise IOError ('\n"Kzz_prof" (the type of Kzz profile) cannot be recongized.\nPlease assign it as "file" or "const" or "JM16" in vulcan_cfg.')
# IF switches for Vz types
if self.vz_prof == 'const': data_atm.vz = np.repeat(self.const_vz,nz-1)
elif self.vz_prof == 'file':
inter_vz = interpolate.interp1d( atm_table['Pressure'], atm_table['vz'], assume_sorted = False, bounds_error=False, fill_value=0 )
data_atm.vz = inter_vz(data_atm.pico[1:-1])
else: raise IOError ('\n"vz_prof" cannot be recongized.\nPlease assign it as "file" or "const" in vulcan_cfg.')
if self.use_Kzz == False:
# store Kzz in data_atm
data_atm.Kzz = np.zeros(nz-1)
if self.use_vz == False:
data_atm.vz = np.zeros(nz-1)
# TEST
# moved to calculating g
# if self.use_settling == True:
# # TESTing settling velocity
# # based on L. D. Cloutman: A Database of Selected Transport Coefficients for Combustion Studies (Table 1.)
# if vulcan_cfg.atm_base == 'N2':
# na = 1.52; a = 1.186e-5; b = 86.54
# elif vulcan_cfg.atm_base == 'H2':
# na = 1.67; a = 1.936e-6; b = 2.187
# elif vulcan_cfg.atm_base == 'CO2':
# print ("NO CO2 viscosity yet! (using N2 instead)")
# na = 1.52; a = 1.186e-5; b = 86.54
# elif vulcan_cfg.atm_base == 'H2O':
# na = 1.5; a = 1.6e-5; b = 0
# elif vulcan_cfg.atm_base == 'O2':
# na = 1.46; a = 2.294e-5; b = 164.4
#
# dmu = a * data_atm.Tco**na /(b + data_atm.Tco) # g cm-1 s-1 dynamic viscosity
#
# for sp in vulcan_cfg.non_gas_sp:
# try:
# rho_p = data_atm.rho_p[sp]
# r_p = data_atm.r_p[sp]
#
# # if sp == 'H2O_l_s':
# # rho_p = data_atm.rho_p_h2o
# # r_p = data_atm.r_p_h2o
# # elif sp == 'H2SO4_l':
# # rho_p = 1.8302
# # r_p = data_atm.r_p_h2so4
# # elif sp == 'H2SO4_l':
# # rho_p = 1.8302
# # r_p = data_atm.r_p_h2so4
#
# except: print (sp + " has not been prescribed size and density!");raise
#
# # Calculating the setteling (terminal) velocity
# data_atm.vs[:,species.index(sp)] = -1. *(2./9*rho_p * r_p**2 * data_atm.g / dmu[1:])
# calculating and storing M(the third body)
data_atm.M = data_atm.pco/(kb*data_atm.Tco)
data_atm.n_0 = data_atm.M.copy()
# moved to f_mu_dz()
# # plot T-P profile
# if vulcan_cfg.plot_TP == True: output.plot_TP(data_atm)
#
# # print warning when T exceeds the valid range of Gibbs free energy (NASA polynomials)
# if np.any(np.logical_or(data_atm.Tco < 200, data_atm.Tco > 6000)): print ('Temperatures exceed the valid range of Gibbs free energy.\n')
return data_atm
# T(P) profile in Heng et al. 2014 (126)
def TP_H14(self, pco, *args_analytical):
# convert args_analytical tuple to a list so we can modify it
T_int, T_irr, ka_0, ka_s, beta_s, beta_l = list(args_analytical)
g = vulcan_cfg.gs
P_b = vulcan_cfg.P_b
# albedo(beta_s) also affects T_irr
albedo = (1.0-beta_s)/(1.0+beta_s)
T_irr *= (1-albedo)**0.25
eps_L = 3./8; eps_L3=1./3; ka_CIA=0
m = pco/g; m_0 = P_b/g; ka_l = ka_0 + ka_CIA*m/m_0
term1 = T_int**4/4*(1/eps_L + m/(eps_L3*beta_l**2)*(ka_0 + ka_CIA*m/(2*m_0) ) )
term2 = (1/(2*eps_L) + scipy.special.expn(2,ka_s*m/beta_s)*(ka_s/(ka_l*beta_s)- (ka_CIA)*m*beta_s/(eps_L3*ka_s*m_0*beta_l**2) ) )
term3 = ka_0*beta_s/(eps_L3*ka_s*beta_l**2)*(1./3 - scipy.special.expn(4,ka_s*m/beta_s))
term4 = 0. #related to CIA
T = (term1 + T_irr**4/8*(term2 + term3 + term4) )**0.25
return T
def mol_mass(self, sp):
''' calculating the molar mass of each species'''
return compo['mass'][compo_row.index(sp)]
def mean_mass(self, var, atm, ni):
mu = np.zeros(nz)
for i in range(ni):
mu += self.mol_mass(species[i]) * var.ymix[:,i]
atm.mu = mu
return atm
def f_mu_dz(self, data_var, data_atm, output): # Initilising mean molecular weight and dz
dz, zco = data_atm.dz, data_atm.zco # pressure defined at interfaces
Tco, pico = data_atm.Tco.copy(), data_atm.pico.copy()
Hp = data_atm.Hp
if vulcan_cfg.rocky == False and self.P_b >= 1e6: # if the lower BC greater than 1bar for gas giants
# Find the index of pico closest to 1bar
pref_indx = min( range(nz+1), key=lambda i: abs(np.log10(pico[i])-6.))
else: pref_indx = 0
# print ("g_s starts from " + str(pico[pref_indx]/1e6) + " bar")
# updating and storing mu
data_atm = self.mean_mass(data_var, data_atm, ni)
mu = data_atm.mu
gs = self.gs
gz = data_atm.g
# updating and storing mu
data_atm = self.mean_mass(data_var, data_atm, ni)
for i in range(pref_indx,nz):
if i == pref_indx:
gz[i] = gs
Hp[i] = kb*Tco[i]/(mu[i]/Navo*gs)
else:
gz[i] = gs * (vulcan_cfg.Rp/(vulcan_cfg.Rp+ zco[i]))**2
Hp[i] = kb*Tco[i]/(mu[i]/Navo*gz[i])
dz[i] = Hp[i] * np.log(pico[i]/pico[i+1]) # pico[i+1] has a lower P than pico[i] (higer height)
zco[i+1] = zco[i] + dz[i] # zco is set zero at 1bar for gas giants
# for pref_indx != zero
if not pref_indx == 0:
for i in range(pref_indx-1,-1,-1):
gz[i] = gs * (vulcan_cfg.Rp/(vulcan_cfg.Rp + zco[i+1]))**2
Hp[i] = kb*Tco[i]/(mu[i]/Navo*gz[i])
dz[i] = Hp[i] * np.log(pico[i]/pico[i+1])
zco[i] = zco[i+1] - dz[i] # from i+1 propogating down to i
zmco = 0.5*(zco + np.roll(zco,-1))
zmco = zmco[:-1]
dzi = 0.5*(dz + np.roll(dz,1))
dzi = dzi[1:]
# for the j grid, dzi[j] from the grid above and dz[j-1] from the grid below
# for the molecular diffsuion
if vulcan_cfg.use_moldiff == True:
Ti = 0.5*(Tco + np.roll(Tco,-1))
data_atm.Ti = Ti[:-1]
Hpi = 0.5*(Hp + np.roll(Hp,-1))
data_atm.Hpi = Hpi[:-1]
# updating and storing dz and dzi
#data_atm.dz = dz
data_atm.dzi = dzi
#data_atm.zco = zco
data_atm.zmco = zmco
data_atm.g, data_atm.gs = gz, gs
data_atm.pref_indx = pref_indx
if self.use_settling == True:
# TESTing settling velocity
# based on L. D. Cloutman: A Database of Selected Transport Coefficients for Combustion Studies (Table 1.)
if vulcan_cfg.atm_base == 'N2':
na = 1.52; a = 1.186e-5; b = 86.54
elif vulcan_cfg.atm_base == 'H2':
na = 1.67; a = 1.936e-6; b = 2.187
elif vulcan_cfg.atm_base == 'CO2':
print ("NO CO2 viscosity yet! (using N2 instead)")
na = 1.52; a = 1.186e-5; b = 86.54
elif vulcan_cfg.atm_base == 'H2O':
na = 1.5; a = 1.6e-5; b = 0
elif vulcan_cfg.atm_base == 'O2':
na = 1.46; a = 2.294e-5; b = 164.4
dmu = a * data_atm.Tco**na /(b + data_atm.Tco) # g cm-1 s-1 dynamic viscosity
for sp in vulcan_cfg.non_gas_sp:
try:
rho_p = data_atm.rho_p[sp]
r_p = data_atm.r_p[sp]
except: print (sp + " has not been prescribed size and density!");raise
# Calculating the setteling (terminal) velocity
gi = 0.5*(data_atm.g + np.roll(data_atm.g,-1))
gi = gi[:-1]
data_atm.vs[:,species.index(sp)] = -1. *(2./9*rho_p * r_p**2 * gi / dmu[1:])
# plot T-P profile
if vulcan_cfg.plot_TP == True: output.plot_TP(data_atm)
# print warning when T exceeds the valid range of Gibbs free energy (NASA polynomials)
if np.any(np.logical_or(data_atm.Tco < 200, data_atm.Tco > 6000)): print ('Temperatures exceed the valid range of Gibbs free energy.\n')
return data_atm
def read_sflux(self, var, atm):
'''reading in stellar stpactal flux at the stellar surface and converting it to the flux on the planet to the uniform grid using trapezoidal integral'''
atm.sflux_raw = np.genfromtxt(vulcan_cfg.sflux_file, dtype=float, skip_header=1, names = ['lambda','flux'])
# for values outside the boundary => fill_value = 0
bins = var.bins
dbin1 = vulcan_cfg.dbin1
dbin2 = vulcan_cfg.dbin2
inter_sflux = interpolate.interp1d(atm.sflux_raw['lambda'], atm.sflux_raw['flux']* (vulcan_cfg.r_star*r_sun/(au*vulcan_cfg.orbit_radius) )**2, bounds_error=False, fill_value=0)
for n, ld in enumerate(var.bins):
var.sflux_top[n] = inter_sflux(ld)
if ld == vulcan_cfg.dbin_12trans: var.sflux_din12_indx = n
# not converting to actinic flux yet *1/(hc/ld)
# Check for energy conservation
# finding the index for the left & right pts that match var.bins in the raw data
raw_flux = atm.sflux_raw['flux']* (vulcan_cfg.r_star*r_sun/(au*vulcan_cfg.orbit_radius) )**2
raw_left_indx = np.searchsorted(atm.sflux_raw['lambda'],bins[0],side='right')
raw_right_indx = np.searchsorted(atm.sflux_raw['lambda'],bins[-1],side='right')-1
sum_orgin = 0
# for checking the trapezoidal error in energy conservation
for n in range(raw_left_indx,raw_right_indx):
sum_orgin += 0.5*(raw_flux[n] + raw_flux[n+1]) * (atm.sflux_raw['lambda'][n+1]- atm.sflux_raw['lambda'][n])
sum_orgin += 0.5 *(inter_sflux(bins[0])+raw_flux[raw_left_indx])* (atm.sflux_raw['lambda'][raw_left_indx]-bins[0])
sum_orgin += 0.5 *(inter_sflux(bins[-1])+raw_flux[raw_right_indx])* (bins[-1]-atm.sflux_raw['lambda'][raw_right_indx])
# dbin_12trans outside the bins
if not 'sflux_din12_indx' in vars(var).keys(): var.sflux_din12_indx = -1
sum_bin = dbin1 * np.sum(var.sflux_top[:var.sflux_din12_indx])
sum_bin -= dbin1 *0.5*(var.sflux_top[0]+var.sflux_top[var.sflux_din12_indx-1])
sum_bin += dbin2 * np.sum(var.sflux_top[var.sflux_din12_indx:])
sum_bin -= dbin2 *0.5*(var.sflux_top[var.sflux_din12_indx]+var.sflux_top[-1])
print ("The stellar flux is interpolated onto uniform grid of " +str(vulcan_cfg.dbin1) + " (<" +str(vulcan_cfg.dbin_12trans)+" nm) and "+str(vulcan_cfg.dbin2)\
+ " (>="+str(vulcan_cfg.dbin_12trans)+" nm)" + " and conserving " + "{:.2f}".format(100* sum_bin/sum_orgin)+" %" + " energy." )
#print (str(100* sum_old/sum_orgin)+" %" )
def mol_diff(self, atm):
'''
choosing the formulea of molecular diffusion for each species
then constucting Dzz(z)
'''
Tco = atm.Tco
n_0 = atm.n_0
# using the value defined on the interface
Tco_i = np.delete((Tco + np.roll(Tco,1))*0.5, 0)
n0_i = np.delete((n_0 + np.roll(n_0,1))*0.5, 0)
if vulcan_cfg.use_moldiff == False:
for i in range(len(species)):
# this is required even without molecular weight
atm.ms[i] = compo[compo_row.index(species[i])][-1]
return
if vulcan_cfg.atm_base == 'H2':
Dzz_gen = lambda T, n_tot, mi: 2.2965E17*T**0.765/n_tot *( 16.04/mi*(mi+2.016)/18.059 )**0.5 # from Moses 2000a
# scaling with (15.27) in [Aeronomy part B by Banks & Kockarts(1973)]
# *( m_ref/mi*(mi+ m_base)/m_tot )**0.5 (m_ref is the molecular mass of the ref-base e.g. CH4 in CH4-H2 in Moses 2000a)
# # thermal diffusion factor (>0 means (heavier) components diffuse toward colder rigions)
if 'H' in species: atm.alpha[species.index('H')] = -0.1 # simplified from Moses 2000a
if 'He' in species: atm.alpha[species.index('He')] = 0.145
for sp in species:
if self.mol_mass(sp) > 4.: atm.alpha[species.index(sp)] = 0.25
elif vulcan_cfg.atm_base == 'N2': # use CH4-N2 in Aeronomy [Banks ] as a reference to scale by the molecular mass
Dzz_gen = lambda T, n_tot, mi: 7.34E16*T**0.75/n_tot *( 16.04/mi*(mi+28.014)/44.054 )**0.5
# # thermal diffusion factor (>0 means (heavier) components diffuse toward colder rigions)
if 'H' in species: atm.alpha[species.index('H')] = -0.25
if 'H2' in species: atm.alpha[species.index('H2')] = -0.25
if 'He' in species: atm.alpha[species.index('He')] = -0.25
if 'Ar' in species: atm.alpha[species.index('Ar')] = 0.17
elif vulcan_cfg.atm_base == 'O2': # use CH4-O2 in Aeronomy [Banks ] as a reference to scale by the molecular mass
Dzz_gen = lambda T, n_tot, mi: 7.51E16*T**0.759/n_tot *( 16.04/mi*(mi+32)/48.04 )**0.5
# # thermal diffusion factor (>0 means (heavier) components diffuse toward colder rigions)
if 'H' in species: atm.alpha[species.index('H')] = -0.25
if 'H2' in species: atm.alpha[species.index('H2')] = -0.25
if 'He' in species: atm.alpha[species.index('He')] = -0.25
if 'Ar' in species: atm.alpha[species.index('Ar')] = 0.17
elif vulcan_cfg.atm_base == 'CO2': # use H2-CO2 in Hu seager as a reference to scale by the molecular mass
Dzz_gen = lambda T, n_tot, mi: 2.15E17*T**0.750/n_tot *( 2.016/mi*(mi+44.001)/46.017 )**0.5
# # thermal diffusion factor (>0 means (heavier) components diffuse toward colder rigions)
if 'H' in species: atm.alpha[species.index('H')] = -0.25
if 'H2' in species: atm.alpha[species.index('H2')] = -0.25
if 'He' in species: atm.alpha[species.index('He')] = -0.25
if 'Ar' in species: atm.alpha[species.index('Ar')] = 0.17
else: raise IOError ('\n Unknow atm_base!')
for i in range(len(species)):
# input should be float or in the form of nz-long 1D array
atm.Dzz[:,i] = Dzz_gen(Tco_i, n0_i, self.mol_mass(species[i]))
# constructing the molecular weight for every species
# this is required even without molecular weight
atm.ms[i] = compo[compo_row.index(species[i])][-1]
# setting the molecuar diffusion of the non-gaseous species to zero
for sp in [_ for _ in vulcan_cfg.non_gas_sp if _ in species]: atm.Dzz[:,species.index(sp)] = 0
def BC_flux(self, atm):
'''
Reading-in the boundary conditions of constant flux (cm^-2 s^-1) at top/bottom
'''
# read in the const top BC
if vulcan_cfg.use_topflux == True:
print ("Using the prescribed constant top flux.")
with open (vulcan_cfg.top_BC_flux_file) as f:
for line in f.readlines():
if not line.startswith("#") and line.strip():
li = line.split()
atm.top_flux[species.index(li[0])] = li[1]
# read in the const bottom BC
if vulcan_cfg.use_botflux == True:
print ("Using the prescribed constant bottom flux.")
with open (vulcan_cfg.bot_BC_flux_file) as f:
for line in f.readlines():
if not line.startswith("#") and line.strip():
li = line.split()
atm.bot_flux[species.index(li[0])] = li[1]
atm.bot_vdep[species.index(li[0])] = li[2]
# using fixed-mixing-ratio BC
if vulcan_cfg.use_fix_sp_bot == True:
print ("Using the prescribed fixed bottom mixing ratios.")
with open (vulcan_cfg.bot_BC_flux_file) as f:
for line in f.readlines():
if not line.startswith("#") and line.strip():
li = line.split()
atm.bot_fix_sp[species.index(li[0])] = li[3]
# TEST condensation
def sp_sat(self, atm):
'''
For all the species in vulcan_cfg.condense_sp, pre-calculating the
saturation varpor pressure (in dyne/cm2) and storing in atm.sat_p.
'''
# the list that the data has been coded
sat_sp_list = ['H2O','NH3','H2SO4','S2','S8' ,'C','H2S' ]
for sp in vulcan_cfg.condense_sp:
if sp not in sat_sp_list: raise IOError ( "No saturation vapor data for " +sp + ". Check the sp_sat function in build_atm.py" )
T = np.copy(atm.Tco)
if sp == "H2O":
# T is in C
T -= 273.
# from Seinfeld & Pandis 2006, P in mbar in the book
a_water = (6.107799961, 4.436518521E-1, 1.428945805E-2, 2.650648471E-4, 3.031240396E-6, 2.034080948E-8, 6.136820929E-11)
a_ice = (6.109177956, 5.034698970E-1, 1.886013408E-2, 4.176223716E-4, 5.824720280E-6, 4.838803174E-8, 1.838826904E-10)
# saturate_p_1 = (T<0)*( a_ice[0] + a_ice[1]*T + a_ice[2]*T**2 + a_ice[3]*T**3 + a_ice[4]*T**4 + a_ice[5]*T**5 + a_ice[6]*T**6 ) +\
# (T>0)*(a_water[0] + a_water[1]*T + a_water[2]*T**2 + a_water[3]*T**3 + a_water[4]*T**4 + a_water[5]*T**5 + a_water[6]*T**6)
# ice from Ackerman&Marley (2001)
c0 = 6111.5; c1 = 23.036; c2 = -333.7; c3 = 279.82
# water from Ackerman&Marley (2001)
w0 = 6112.1; w1 = 18.729; w2 = -227.3; w3 = 257.87
saturate_p = (T<0)*( c0 * np.exp( (c1*T + T**2/c2)/(T + c3) ) ) + (T>0)*(w0 * np.exp( (w1*T + T**2/w2)/(T + w3) ) )
atm.sat_p[sp] = saturate_p
#atm.sat_p[sp] = c0 * np.exp( (c1*T + T**2/c2)/(T + c3) )
#atm.sat_p[sp] = moses_ice
elif sp == "NH3":
# from Weast (1971) in bar
c0 = 10.53; c1 = -2161.0; c2 = -86596.0
saturate_p = np.exp(c0 + c1/T + c2/T**2)
atm.sat_p[sp] = saturate_p * 1.e6
elif sp == "H2SO4":
# change to Kulmala later
p_ayers = np.e**(-10156./T + 16.259) # in atm
atm.sat_p[sp] = p_ayers * 1.01325*1e6 # arm to cgs
elif sp == "S2":
atm.sat_p[sp] = np.zeros(nz)
# from Zahnle 2017 (refitted from Lyons 2008)
atm.sat_p[sp][T<413] = np.exp(27. - 18500./T[T<413]) *1e6 # in bar => cgs
atm.sat_p[sp][T>=413] = np.exp(16.1 - 14000./T[T>=413]) *1e6
elif sp == "S4":
atm.sat_p[sp] = np.zeros(nz)
# from Lyons 2008
atm.sat_p[sp] = 10**(6.0028 -6047.5/T) *1.01325e6 # atm to vgs
elif sp == "S8":
atm.sat_p[sp] = np.zeros(nz)
# from Zahnle 2017 (refitted from Lyons 2008)
atm.sat_p[sp][T<413] = np.exp(20. - 11800./T[T<413]) *1e6 # in bar => cgs
atm.sat_p[sp][T>=413] = np.exp(9.6 - 7510./T[T>=413]) *1e6
elif sp == "C":
atm.sat_p[sp] = np.zeros(nz)
# from NIST (dyna cm^-2)
a = 3.27860E+01
b = -8.65139E+04
c = 4.80395E-01
atm.sat_p[sp] = np.exp(a+b/(atm.Tco +c) )
elif sp == "H2S":
# from Giauque and Blue(1936) in cmHg (adoped in Atreya's book)
h2s_ice_log10 = -1329./T + 9.28588 - 0.0051263*T # 164.9 <= T <= 187.6
h2s_l_log10 = -1145./T + 7.94746 - 0.00322*T # 187.6 < T <= 213.2
saturate_p = 10**( (T <= 187.6)*h2s_ice_log10 + (T > 187.6)*h2s_l_log10 )
atm.sat_p[sp] = saturate_p * 0.001333 * 1.e6
if __name__ == "__main__":
print("This module stores classes for constructing atmospheric structure \
and initializing its chemical composition from the desinated elemental abudance.")