# this calcuate the equilirbium abundance @ T
# however this attr is not defined for fully ionized species...
# fix that later, take this as 1 for now first
#ion_frac = ion.IoneqOne
ion_frac = 1.0
# ion.Abundance is the elemental abundance relative to hydrogen
init_values[s.name] = ion_frac * init_array * ion.Abundance
# in case something is negative or super small:
init_values[s.name][init_values[s.name] < tiny] = tiny
init_values['de'] = init_array * 0.0
init_values = ion_by_ion.convert_to_mass_density(init_values)
init_values['de'] = ion_by_ion.calculate_free_electrons(init_values)
init_values['density'] = ion_by_ion.calculate_total_density(init_values)
number_density = ion_by_ion.calculate_number_density(init_values)
# calculate ge (very crudely)
gamma = 5.0/3.0
init_values['ge'] = ((temperature * number_density * kboltz)
/ (init_values['density'] * mh * (gamma - 1)))
# Write the initial conditions file
# IF you need to use the Makefile, and c-library
# you will have to specified the library_path
library_path = {}
library_path["CVODE_PATH"] = "/home/kwoksun2/cvode-3.1.0/instdir"
library_path["HDF5_PATH"] = "/home/kwoksun2/anaconda3"
library_path["SUITESPARSE_PATH"] = "/home/kwoksun2/SuiteSparse"
# setting initial conditions
init_array = np.ones(NCELLS) * density
init_values = dict()
init_values["H_1"] = (1 - X) * init_array
init_values['H_2'] = X * init_array
init_values['H_m0'] = init_array * tiny
init_values['He_1'] = init_array * tiny
init_values['He_2'] = init_array * tiny
init_values['He_3'] = init_array * tiny
init_values['H2_1'] = init_array * tiny
init_values['H2_2'] = init_array * tiny
init_values['de'] = init_array * 0.0
# update and calculate electron density and etc with the handy functions
total_density = primordial.calculate_total_density(init_values)
init_values = primordial.convert_to_mass_density(init_values)
init_values['de'] = primordial.calculate_free_electrons(init_values)
init_values['density'] = primordial.calculate_total_density(init_values)
number_density = primordial.calculate_number_density(init_values)
# set up initial temperatures values used to define ge
init_values['T'] = temperature
# calculate ge (very crudely, no H2 help here)
gamma = 5.0 / 3.0
init_values['ge'] = ((temperature * number_density * kboltz) /
(init_values['density'] * mh * (gamma - 1)))
# Write the initial conditions file
# IF you need to use the Makefile, and c-library
tiny = 1e-10
init_array = np.ones(NCELLS) * density
init_values = dict()
init_values['OII'] = X * init_array
init_values['OIII'] = init_array * X
init_values['OIV'] = init_array * X
init_values['OV'] = init_array * X
init_values['OVI'] = init_array * X
init_values['OVII'] = init_array * X
init_values['OVIII'] = init_array * X
init_values['OIX'] = init_array * X
init_values['de'] = init_array * 0.0
total_density = oxygen.calculate_total_density(init_values, ("OI", ))
init_values["OI"] = init_array.copy() - total_density
init_values = oxygen.convert_to_mass_density(init_values)
init_values['de'] = oxygen.calculate_free_electrons(init_values)
init_values['density'] = oxygen.calculate_total_density(init_values)
number_density = oxygen.calculate_number_density(init_values)
# set up initial temperatures values used to define ge
init_values['T'] = temperature
# calculate ge (very crudely, no H2 help here)
gamma = 5.0 / 3.0
init_values['ge'] = ((temperature * number_density * kboltz) /
(init_values['density'] * mh * (gamma - 1)))
# Write the initial conditions file
init_values['H_2'] = 0.056 * init_array
init_values['I2_1'] = 8.0e-8 * init_array * (126 * 2)
init_values['H2O_1'] = 1.0 * init_array * (18)
init_values['HOIO_1'] = 9.0e-11 * init_array * (126 + 32 + 1)
init_values['IO3m_0'] = 0.01 * init_array * (1 + 16 * 3)
init_values['O2_1'] = 2.5e3 * init_array * (16 * 2)
init_values['CH2_COOH2_1'] = 0.0015 * init_array * (12 + 2 +
(12 + 16 * 2 + 1) * 2)
init_values['CHI_COOH2_1'] = 1.0e-20 * init_array * (12 + 126 +
(12 + 16 * 2 + 1) * 2)
init_values["H2O2_1"] = 0.33 * init_array * (2 + 16) * 2
print(new.required_species)
total_density = new.calculate_total_density(init_values)
init_values = new.convert_to_mass_density(init_values)
init_values['de'] = new.calculate_free_electrons(init_values)
init_values['density'] = init_array # new.calculate_total_density(init_values)
number_density = new.calculate_number_density(init_values)
# set up initial temperatures values used to define ge
init_values['T'] = temperature
# calculate ge (very crudely, no H2 help here)
gamma = 5.0 / 3.0
init_values['ge'] = ((temperature * number_density * kboltz) /
(init_values['density'] * mh * (gamma - 1)))
# Write the initial conditions file
# IF you need to use the Makefile, and c-library
tiny = 1e-10
init_array = np.ones(NCELLS) * density
init_values = dict()
init_values['us_H_1'] = init_array * X
init_values['us_H2_1'] = init_array * X
init_values['us_e_0'] = init_array * 0.0
print(init_values)
#print sorted(umist.reactions.values())
for species in umist.required_species:
if species.name not in init_values:
init_values[species.name] = init_array * 0.0
total_density = umist.calculate_total_density(init_values)
init_values = umist.convert_to_mass_density(init_values)
init_values['us_e_0'] = umist.calculate_free_electrons(init_values)
init_values['density'] = umist.calculate_total_density(init_values)
number_density = umist.calculate_number_density(init_values)
# set up initial temperatures values used to define ge
init_values['T'] = temperature
# calculate ge (very crudely, no H2 help here)
gamma = 5.0 / 3.0
init_values['ge'] = ((temperature * number_density * kboltz) /
(init_values['density'] * mh * (gamma - 1)))
print(init_values)
init_values['T'] = temperature
start_neutral = False
if start_neutral:
init_values['OII'] = X * init_array
init_values['OIII'] = init_array * X
init_values['OIV'] = init_array * X
init_values['OV'] = init_array * X
init_values['OVI'] = init_array * X
init_values['OVII'] = init_array * X
init_values['OVIII'] = init_array * X
init_values['OIX'] = init_array * X
init_values['de'] = init_array * 0.0
total_density = combined.calculate_total_density(init_values, ("OI", ))
init_values["OI"] = init_array.copy() - total_density
init_values = combined.convert_to_mass_density(init_values)
else:
# start CIE
import chianti.core as ch
import chianti.util as chu
for s in sorted(combined.required_species):
if s.name != 'ge':
if s.name == 'de':
continue
else:
print s.name, s.number, s.free_electrons + 1
ion_name = chu.zion2name(np.int(s.number),
np.int(s.free_electrons + 1))
def Init_values(temperature, density, n_species=9, cooling=True):
""" Create a initial value dictionary,
for a given temperature, density, number of species
Args:
temperature -- in Kelvin
density -- in amu / cm**3
n_species -- number of species (6/9)
cooling
Returns:
init_values: initial value dictionary with
self-consistent energy/ electron density
primordial : chemical_network classes
"""
# initialize and setup the network
dengo.primordial_rates.setup_primordial()
primordial = ChemicalNetwork()
if n_species == 9:
for i in range(23):
try:
primordial.add_reaction("k{0:02d}".format(i + 1))
except:
pass
else:
for i in range(6):
try:
primordial.add_reaction("k{0:02d}".format(i + 1))
except:
pass
# the temperature array required to interpolates the rates
primordial.init_temperature((1e0, 1e5))
tiny = 1.0e-20
# init_array are is in fractional abundances
init_values = dict()
if n_species == 6:
# 6-species model
init_values["He_1"] = density * (1.0 - 0.76) / 2.
init_values["He_2"] = density * (1.0 - 0.76) / 2.
init_values["He_3"] = np.array([tiny])
init_values["H_1"] = density * (0.76) / 2.
init_values['H_2'] = density * (0.76) / 2.
else:
# 9-species model
init_values["He_1"] = density * (1.0 - 0.76) / 2.0
init_values["He_2"] = density * (1.0 - 0.76) / 2.0
init_values["He_3"] = np.array([tiny])
init_values["H_1"] = density * (0.76) / 3.
init_values['H_2'] = density * (0.76) / 3.
init_values["H_m0"] = np.array([tiny])
init_values["H2_1"] = density * (0.76) / 3.
init_values["H2_2"] = np.array([tiny])
# now everything in mass density
init_values['de'] = primordial.calculate_free_electrons(init_values)
# one signle value: again mass density
init_values['density'] = primordial.calculate_total_density(init_values)
num_den = {}
for sp in primordial.required_species:
try:
num_den[sp.name] = init_values[sp.name] / sp.weight
except:
pass
# set up initial temperatures values used to define ge
init_values['T'] = temperature
# calculate gammaH2
x = 6100.0 / temperature
gammaH2 = 2.0 / (5.0 + 2.0 * x * x / (numpy.exp(x) - 1)**2.0) + 1
gamma_factor = primordial.gamma_factor().subs(num_den).subs({
'gammaH2':
gammaH2,
'gamma':
5. / 3.,
'T':
temperature
})
ge = ((temperature * kboltz) * gamma_factor /
(init_values['density'] * mh))
T = init_values['density'] * ge * mh / kboltz / gamma_factor
print("difference in temperature:", T - temperature)
init_values['ge'] = numpy.array([numpy.float64(ge)])
if cooling:
for cooling_action in cooling_registry:
k = cooling_registry[cooling_action]
if (k.species).issubset(primordial.required_species):
if k.name != "cie_cooling":
print("adding:", k.name, k.equation)
primordial.add_cooling(cooling_action)
print('---------------------------')
return init_values, primordial
