def setup_predator_prey_network():
setup_predator_prey_rates()
cN = ChemicalNetwork()
cN.add_reaction("exp_growth_prey")
cN.add_reaction("predation")
cN.add_reaction("natural_death_predator")
# this shouldnt be compulsory...
cN.init_temperature((1e0, 1e8))
return cN
def __init__(self):
primordial_simplified = ChemicalNetwork()
primordial_simplified.add_reaction("k01")
primordial_simplified.add_reaction("k22")
primordial_simplified.add_cooling("h2formation")
primordial_simplified.add_cooling("gloverabel08")
self.network = primordial_simplified
self.solution = TestChemicalNetworkSolution()
from dengo.chemical_network import \
ChemicalNetwork, \
reaction_registry, \
cooling_registry
import dengo.primordial_rates, dengo.primordial_cooling
from dengo.chemistry_constants import tiny, kboltz, mh
# from dengo.known_species import *
# If only a subset of species are wanted put them here
# and change the commented lines below
want = ("HI", "HII", "de", "ge")
primordial = ChemicalNetwork()
#primordial.add_energy_term()
# Set to false if intermediate solution output is not wanted
primordial.write_intermediate_solutions = True
#for ca in cooling_registry.values():
#if not all(sp.name in want for sp in ca.species): continue
# primordial.add_cooling(ca)
for i, rname in enumerate(sorted(reaction_registry)):
s = reaction_registry[rname]
#if not all(sp.name in want for sp in s.species): continue
primordial.add_reaction(s)
# This defines the temperature range for the rate tables
primordial.init_temperature((1e0, 1e8))
# Generate initial conditions (switch to False to disable this)
from dengo.chemical_network import \
ChemicalNetwork, \
reaction_registry, \
cooling_registry
import dengo.primordial_rates, dengo.primordial_cooling
import dengo.oxygen_rates, dengo.oxygen_cooling
from dengo.chemistry_constants import tiny, kboltz, mh
from dengo.known_species import *
NCELLS = 4
density = 1.0
temperature = np.logspace(4, 6.7, NCELLS)
temperature[:] = 1e7
X = 1e-3
oxygen = ChemicalNetwork()
oxygen.add_energy_term()
for ca in cooling_registry.values():
if ca.name.startswith("O"):
oxygen.add_cooling(ca)
for s in reaction_registry.values():
if s.name.startswith("O"):
oxygen.add_reaction(s)
# This defines the temperature range for the rate tables
oxygen.init_temperature((1e0, 1e8))
tiny = 1e-10
from dengo.chemical_network import ChemicalNetwork, reaction_registry
import dengo.primordial_rates
primordial = ChemicalNetwork()
for i in range(23):
n = "k%02i" % (i+1)
if n in reaction_registry:
primordial.add_reaction(n)
print "These species are required:"
print "\n".join([s.name for s in sorted(primordial.required_species)])
for species in primordial.required_species:
print "Querying: ", species
for rxn in primordial.species_reactions(species):
print " ", rxn
for rxn in primordial:
write_reaction(rxn)
for species in primordial.required_species:
write_species_deriv(species, primordial.species_reactions(species))
cooling_registry
import dengo.new_rates
from dengo.chemistry_constants import tiny, kboltz, mh
#from dengo.known_species import *
import os
os.environ["HDF5_DIR"] = "/home/kwoksun2/anaconda3"
NCELLS = 1
density = 1e0
temperature = np.logspace(2, 4, NCELLS)
temperature[:] = 2e3
X = 0.5
dengo.new_rates.setup_new()
new = ChemicalNetwork()
new.add_reaction("I01")
new.add_reaction("I01_re")
new.add_reaction("I02")
new.add_reaction("I03")
new.add_reaction("I04")
new.add_reaction("I05")
new.add_reaction("C05")
new.add_reaction("D01")
# This defines the temperature range for the rate tables
new.init_temperature((1e0, 1e8))
init_array = np.ones(NCELLS) * density
init_values = dict()
init_values["HOI_1"] = 8.0e-11 * init_array * (200)
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
from dengo.ion_by_ion import setup_ionization
from dengo.chemistry_constants import tiny, kboltz, mh
import numpy as np
from dengo.reaction_classes import AtomicSpecies
import os
os.environ["HDF5_DIR"] = '/home/kwoksun2/anaconda3'
NCELLS = 1
density = 1.0
#* 1.67e-24
temperature = np.logspace(2, 8, NCELLS)
temperature[:] = 5e6
X = 1e-8
ion_by_ion = ChemicalNetwork(write_intermediate = False,
stop_time = 3.1557e13)
HI = AtomicSpecies("H", 0.0)
HII = AtomicSpecies("H", 1.0)
HeI = AtomicSpecies("He", 0.0)
HeII = AtomicSpecies("He", 1.0)
de = species_registry['de']
ion_by_ion.add_species(de)
ion_by_ion.add_species(HI)
ion_by_ion.add_species(HII)
ion_by_ion.add_species(HeI)
ion_by_ion.add_species(HeII)
#ion_by_ion.add_species('O_1')
#ion_by_ion.add_species('O_2')
#ion_by_ion.add_species('O_3')
#ion_by_ion.add_species('O_4')
from dengo.chemical_network import \
ChemicalNetwork, \
reaction_registry, \
cooling_registry
import dengo.primordial_rates, dengo.primordial_cooling
from dengo.chemistry_constants import tiny, kboltz, mh
NCELLS = 4
density = 1e7
temperature = np.logspace(2, 4, NCELLS)
temperature[:] = 2e3
X = 0.5
dengo.primordial_rates.setup_primordial()
primordial = ChemicalNetwork()
primordial.add_reaction("k01")
primordial.add_reaction("k02")
# This defines the temperature range for the rate tables
primordial.init_temperature((1e0, 1e8))
tiny = 1e-10
init_array = np.ones(NCELLS) * density
init_values = dict()
init_values['HII'] = X * init_array
init_values['de'] = init_array * 0.0
#total_density = primordial.calculate_total_density(init_values, ("HI",))
cooling_registry
import dengo.new_rates
from dengo.chemistry_constants import tiny, kboltz, mh
#from dengo.known_species import *
import os
os.environ["HDF5_DIR"] = "/home/kwoksun2/anaconda3"
NCELLS = 1
density = 1e0
temperature = np.logspace(2, 4, NCELLS)
temperature[:] = 2e3
X = 0.5
dengo.new_rates.setup_new()
new = ChemicalNetwork()
new.add_reaction("I01")
new.add_reaction("I01_re")
new.add_reaction("I02")
new.add_reaction("I03")
new.add_reaction("I04")
new.add_reaction("I05")
new.add_reaction("C05")
new.add_reaction("D01")
# This defines the temperature range for the rate tables
new.init_temperature((1e0, 1e8))
init_array = np.ones(NCELLS) * density
init_values = dict()
init_values["HOI_1"] = 8.0e-11 * init_array * (200)
import numpy as np
from dengo.chemical_network import \
ChemicalNetwork, \
reaction_registry, \
cooling_registry
import dengo.primordial_rates, dengo.primordial_cooling
from dengo.chemistry_constants import tiny, kboltz, mh
from dengo.known_species import *
NCELLS = 4
density = 1e7
temperature = np.logspace(2, 4, NCELLS)
temperature[:] = 2e3
X = 0.5
primordial = ChemicalNetwork()
primordial.add_energy_term()
primordial.add_cooling("brem")
primordial.add_cooling("reHII")
primordial.add_cooling("reHeIII")
primordial.add_cooling("gloverabel08")
primordial.add_cooling("ceHI")
primordial.add_cooling("h2formation")
primordial.add_cooling("reHeII2")
primordial.add_cooling("reHeII1")
primordial.add_cooling("ciHeIS")
primordial.add_cooling("ceHeII")
primordial.add_cooling("ciHI")
primordial.add_cooling("ceHeI")
primordial.add_cooling("gammah")
import dengo.nitrogen_rates, dengo.nitrogen_cooling
import dengo.oxygen_rates, dengo.oxygen_cooling
import dengo.neon_rates, dengo.neon_cooling
import dengo.magnesium_rates, dengo.magnesium_cooling
import dengo.silicon_rates, dengo.silicon_cooling
import dengo.sulfur_rates, dengo.sulfur_cooling
from dengo.chemistry_constants import tiny, kboltz, mh
import numpy as np
NCELLS = 1
density = 1.0
temperature = np.logspace(4, 6.7, NCELLS)
temperature[:] = 5e6
X = 1e-3
combined = ChemicalNetwork()
combined.add_energy_term()
for ca in cooling_registry.values():
if ca.name.startswith("C") \
or ca.name.startswith("N") \
or ca.name.startswith("O") \
or ca.name.startswith("Ne") \
or ca.name.startswith("Mg") \
or ca.name.startswith("Si") \
or ca.name.startswith("S"):
combined.add_cooling(ca)
combined.add_cooling("brem")
combined.add_cooling("reHII")
combined.add_cooling("reHeIII")
from dengo.chemical_network import \
ChemicalNetwork, \
reaction_registry, \
cooling_registry
from dengo.reaction_classes import index_i, count_m
import dengo.primordial_rates, dengo.primordial_cooling
import dengo.oxygen_rates, dengo.oxygen_cooling
from dengo.write_rate_reader import create_rate_tables, create_rate_reader
import sympy
from sympy.printing import print_ccode
oxygen = ChemicalNetwork()
for ca in cooling_registry.values():
if ca.name.startswith("o_"):
oxygen.add_cooling(ca)
print "These species are required for cooling alone:"
print "\n".join([s.name for s in sorted(oxygen.required_species)])
for s in reaction_registry.values():
if s.name.startswith("o_"):
oxygen.add_reaction(s)
print "These species are required for chemistry and cooling:"
print "\n".join([s.name for s in sorted(oxygen.required_species)])
functions = []
cooling = sum(v.equation for n, v in sorted(oxygen.cooling_actions.items()))
for species in oxygen.required_species:
from dengo.chemical_network import \
ChemicalNetwork, \
reaction_registry, \
cooling_registry
import dengo.primordial_rates, dengo.primordial_cooling
from dengo.chemistry_constants import tiny, kboltz, mh
NCELLS = 4
density = 1e7
temperature = np.logspace(2, 4, NCELLS)
temperature[:] = 2e3
X = 0.75
dengo.primordial_rates.setup_primordial()
primordial = ChemicalNetwork()
primordial.add_reaction("k01")
primordial.add_reaction("k02")
primordial.add_reaction("k03")
primordial.add_reaction("k04")
primordial.add_reaction("k05")
primordial.add_reaction("k06")
# This defines the temperature range for the rate tables
primordial.init_temperature((1e0, 1e8))
tiny = 1e-10
init_array = np.ones(NCELLS) * density
init_values = dict()
def setup_network():
"""Initial a ChemicalNetwork object
for primordial network 9-species model
Return:
primordial: ChemicalNetwork with primordial reactions and cooling
"""
# this register all the rates specified in `primordial_rates.py`
dengo.primordial_rates.setup_primordial()
# initialize the chmical network object
primordial = ChemicalNetwork()
# add all the reactions
primordial.add_reaction("k01")
primordial.add_reaction("k02")
primordial.add_reaction("k03")
primordial.add_reaction("k04")
primordial.add_reaction("k05")
primordial.add_reaction("k06")
primordial.add_reaction("k07")
primordial.add_reaction("k08")
primordial.add_reaction("k09")
primordial.add_reaction("k10")
primordial.add_reaction("k11")
primordial.add_reaction("k12")
primordial.add_reaction("k13")
primordial.add_reaction("k14")
primordial.add_reaction("k15")
primordial.add_reaction("k16")
primordial.add_reaction("k17")
primordial.add_reaction("k18")
primordial.add_reaction("k19")
primordial.add_reaction("k21")
primordial.add_reaction("k22")
primordial.add_reaction("k23")
primordial.add_cooling("brem")
primordial.add_cooling("reHII")
primordial.add_cooling("reHeIII")
primordial.add_cooling("gloverabel08")
primordial.add_cooling("ceHI")
primordial.add_cooling("h2formation")
primordial.add_cooling("h2formation_extra")
primordial.add_cooling("reHeII2")
primordial.add_cooling("reHeII1")
primordial.add_cooling("ciHeIS")
primordial.add_cooling("ceHeII")
primordial.add_cooling("ciHI")
primordial.add_cooling("ceHeI")
primordial.add_cooling("gammah")
primordial.add_cooling("ciHeI")
primordial.add_cooling("ciHeII")
primordial.add_cooling("cie_cooling")
primordial.add_cooling("compton")
# This defines the temperature range for the rate tables
primordial.init_temperature((1e0, 1e8))
primordial.enforce_conservation = True
return primordial
ChemicalNetwork, \
reaction_registry, \
cooling_registry
import dengo.primordial_rates, dengo.primordial_cooling
import dengo.carbon_rates, dengo.carbon_cooling
from dengo.write_rate_reader import \
create_rate_tables, \
create_rate_reader, \
create_initial_conditions
from dengo.chemistry_constants import tiny, kboltz, mh
# If only a subset of species are wanted put them here
# and change the commented lines below
want = ('CIII', 'CIV', 'CV', 'de', 'ge')
carbon = ChemicalNetwork()
carbon.add_energy_term()
# for ca in cooling_registry.values():
# # The following line can be used to specify a subset of species
# #if all(sp.name in want for sp in ca.species):
# if ca.name.startswith("C"):
# carbon.add_cooling(ca)
for s in reaction_registry.values():
# The following line can be used to specify a subset of species
#if all(sp.name in want for sp in s.species):
if s.name.startswith("C"):
carbon.add_reaction(s)
# This defines the temperature range for the rate tables
ChemicalNetwork, \
reaction_registry, \
cooling_registry
from dengo.primordial_rates import setup_primordial
import dengo.primordial_cooling
from dengo.ion_by_ion import setup_ionization
from dengo.chemistry_constants import tiny, kboltz, mh
import numpy as np
NCELLS = 1
density = 1e-3 * 1.67e-24
temperature = np.logspace(4, 6.7, NCELLS)
temperature[:] = 5e6
X = 1e-3
ion_by_ion = ChemicalNetwork(write_intermediate=False, stop_time=3.1557e13)
ion_by_ion.add_species("de")
#for atom in ["O", "C", "Si", "Mg", "N", "S", "He", "Ne", "H"]:
for atom in ["H", "O", "He"]:
s, c, r = setup_ionization(atom)
ion_by_ion.add_collection(s, c, r)
#ion_by_ion.add_collection(s, [], r)
# ion_by_ion.add_cooling('compton')
#s, c, r = setup_primordial()
#ion_by_ion.add_collection(s, c, r)
# This defines the temperature range for the rate tables
ion_by_ion.init_temperature((1e0, 1e12))
import numpy as np
from dengo.chemical_network import \
ChemicalNetwork, \
reaction_registry, \
cooling_registry
import dengo.umist_rates
from dengo.get_rates import setup_umist_species, setup_umist_reactions
from dengo.chemistry_constants import tiny, kboltz, mh
NCELLS = 4
density = 1.0
temperature = np.logspace(1, 3, NCELLS)
temperature[:] = 1e2
X = 1e-3
umist = ChemicalNetwork()
umist.skip_weight += ("us_e_0", )
# This defines the temperature range for the rate tables
umist.init_temperature((1e0, 1e3))
# Get UMIST rates for a bunch of species for an example network
desired_species = [("H", 1), ("H2", 2), ("e-", 1)]
added_species = set([])
for name, weight in desired_species:
s, c, r = setup_umist_species(name, weight)
print "ADDED", s
added_species.update(s)
umist.add_collection(s, c, r)
import numpy as na
import h5py
from dengo.chemical_network import ChemicalNetwork
from dengo.reaction_classes import Species, chianti_rate, reaction_registry, species_registry
import dengo.primordial_rates
import dengo.oxygen_rates
from dengo.oxygen_cooling import cooling_rates_table, cooling_action_table
oxygen_network = ChemicalNetwork()
for rate in sorted(reaction_registry):
if rate.startswith("o_"):
oxygen_network.add_reaction(rate)
print "These species are required:"
print "\n".join([s.name for s in sorted(oxygen_network.required_species)])
for species in oxygen_network.required_species:
print "Querying: ", species
for rxn in oxygen_network.species_reactions(species):
print " ", rxn
for rxn in oxygen_network:
write_reaction(rxn)
for species in oxygen_network.required_species:
print species.name
write_species_deriv(species, oxygen_network.species_reactions(species))
# Define the temperature we want rate values for
Tlog_bounds = (1, 9)
reaction_registry, \
cooling_registry
import dengo.umist_rates
from dengo.get_rates import setup_umist_species, setup_umist_reactions
from dengo.chemistry_constants import tiny, kboltz, mh
import os
os.environ['HDF5_DIR'] = '/home/kwoksun2/anaconda2/'
NCELLS = 1
density = 1.0e0
temperature = np.logspace(1, 3, NCELLS)
temperature[:] = 1e3
X = 1e-2
umist = ChemicalNetwork()
umist.skip_weight += ("us_e_0", )
# This defines the temperature range for the rate tables
umist.init_temperature((1e0, 1e3))
# Get UMIST rates for a bunch of species for an example network
desired_species = [("H", 1), ("H2", 2), ("e-", 1)]
added_species = set([])
for name, weight in desired_species:
s, c, r = setup_umist_species(name, weight)
print("ADDED", s)
added_species.update(s)
umist.add_collection(s, c, r)
cooling_registry
import dengo.primordial_rates, dengo.primordial_cooling
from dengo.chemistry_constants import tiny, kboltz, mh
import os
# this is required to compiled cython
os.environ["HDF5_DIR"] = "/home/kwoksun2/anaconda3"
NCELLS = 4
density = 1e12
temperature = np.logspace(2, 4, NCELLS)
temperature[:] = 2e3
X = 1.0e-4
dengo.primordial_rates.setup_primordial()
primordial = ChemicalNetwork()
#primordial.add_energy_term()
# add the neccessary cooling and reactions
primordial.add_reaction("k01")
primordial.add_reaction("k02")
primordial.add_reaction("k03")
primordial.add_reaction("k04")
primordial.add_reaction("k05")
primordial.add_reaction("k06")
primordial.add_reaction("k07")
primordial.add_reaction("k08")
primordial.add_reaction("k09")
primordial.add_reaction("k10")
primordial.add_reaction("k11")
primordial.add_reaction("k12")
from dengo.chemical_network import \
ChemicalNetwork, \
reaction_registry, \
cooling_registry
from dengo.reaction_classes import index_i, count_m
import dengo.primordial_rates, dengo.primordial_cooling
from dengo.write_rate_reader import create_rate_tables, create_rate_reader
import sympy
from sympy.utilities.codegen import codegen
from sympy.printing import print_ccode
primordial = ChemicalNetwork()
for ca in cooling_registry.values():
primordial.add_cooling(ca)
print "These species are required for cooling alone:"
print "\n".join([s.name for s in sorted(primordial.required_species)])
for s in reaction_registry.values():
primordial.add_reaction(s)
print "These species are required for chemistry and cooling:"
print "\n".join([s.name for s in sorted(primordial.required_species)])
functions = []
cooling = sum(v.equation
for n, v in sorted(primordial.cooling_actions.items()))
for species in primordial.required_species:
print