def cooling_rate(field, data, my_chemistry):
fc = FluidContainer(my_chemistry, data["PartType0", "Masses"].shape[0])
fc["density"][:] = data["PartType0", "Density"]
fc["metal"][:] = data["PartType0", "Density"] * data["PartType0",
"Metallicity"]
fc["x-velocity"][:] = data["PartType0", "Velocities"][:, 0]
fc["y-velocity"][:] = data["PartType0", "Velocities"][:, 1]
fc["z-velocity"][:] = data["PartType0", "Velocities"][:, 2]
fc["energy"][:] = data["PartType0", "InternalEnergy"]
fc.calculate_temperature()
fc.calculate_cooling_time()
dt = yt.units.s
fc.solve_chemistry(dt.value / my_chemistry.time_units)
de = (data["PartType0", "InternalEnergy"].value - fc["energy"])
dE = de * data["PartType0", "Masses"].value
dE *= yt.units.Msun * yt.units.pc**2 / yt.units.Myr**2
dE_dt = dE / dt
return dE_dt
def temperature(field, data, my_chemistry):
fc = FluidContainer(my_chemistry, data["PartType0", "Masses"].shape[0])
fc["density"][:] = data["PartType0", "Density"]
fc["metal"][:] = data["PartType0", "Density"] * data["PartType0",
"Metallicity"]
fc["x-velocity"][:] = data["PartType0", "Velocities"][:, 0]
fc["y-velocity"][:] = data["PartType0", "Velocities"][:, 1]
fc["z-velocity"][:] = data["PartType0", "Velocities"][:, 2]
fc["energy"][:] = data["PartType0", "InternalEnergy"]
fc.calculate_temperature()
return fc["temperature"] * yt.units.Kelvin
def prepare_model(cds, start_time, profile_index, fc=None):
time_data = cds.data["time"]
time_index = np.abs(time_data - start_time).argmin()
if ('data', 'specific_thermal_energy') not in cds.field_list:
cds.add_field(('data', 'specific_thermal_energy'),
sampling_type="local",
function=_specific_thermal_energy,
units="erg/g")
efields = [
"external_pressure", "dark_matter", "metallicity",
"turbulent_velocity", "H2_p0_dissociation_rate",
"H_p0_ionization_rate", "He_p0_ionization_rate",
"He_p1_ionization_rate", "photo_gamma"
]
external_data = {}
field_list = [field for field in cds.field_list if field[1] != "time"]
if ('data', 'specific_thermal_energy') not in field_list:
field_list.append(('data', 'specific_thermal_energy'))
field_data = dict((field, cds.data[field][time_index:, profile_index])
for field in field_list)
if fc is None:
fc = FluidContainer(cds.grackle_data, 1)
fields = _get_needed_fields(fc.chemistry_data)
for gfield in fields:
yfield, units = _field_map[gfield]
pfield = ("data", yfield[1])
fc[gfield][:] = field_data[pfield][0].to(units)
# get external data to be used in fluid container
if pfield[1] in efields:
efields.pop(efields.index(pfield[1]))
external_data[gfield] = field_data[pfield].to(units).d
# get extra solely external data fields
for efield in efields:
yfield, units = _field_map[efield]
external_data[efield] = field_data[yfield].to(units).d
if 'de' in fc:
fc['de'] *= (mp / me).d
field_data["time"] = time_data[time_index:] - time_data[time_index]
external_data["time"] = field_data["time"].to("s").d / \
fc.chemistry_data.time_units
return fc, external_data, field_data
def _data_to_fc(data, size=None, fc=None):
if size is None:
size = data['gas', 'density'].size
if fc is None:
fc = FluidContainer(data.ds.grackle_data, size)
flatten = len(data['gas', 'density'].shape) > 1
fields = _get_needed_fields(fc.chemistry_data)
for gfield in fields:
yfield, units = _field_map[gfield]
fdata = data[yfield].to(units)
if flatten:
fdata = fdata.flatten()
fc[gfield][:] = fdata
if 'de' in fc:
fc['de'] *= (mp / me)
return fc
my_chemistry.density_units = mass_hydrogen_cgs # rho = 1.0 is 1.67e-24 g
my_chemistry.length_units = cm_per_mpc # 1 Mpc in cm
my_chemistry.time_units = sec_per_Myr # 1 Myr in s
my_chemistry.velocity_units = my_chemistry.a_units * \
(my_chemistry.length_units / my_chemistry.a_value) / \
my_chemistry.time_units
# set initial density and temperature
initial_temperature = 100.
#initial_density = 1.0e3/0.9 * mass_hydrogen_cgs
initial_density = 1.e3 * mass_hydrogen_cgs
final_time = 3.2e3 # 0.05 #1.e3 #1. # 1.e3 # 1.e3 # in Myr
rval = my_chemistry.initialize()
fc = FluidContainer(my_chemistry, 1)
fc["density"][:] = initial_density / my_chemistry.density_units
fc["HII"][:] = tiny_number * fc["density"]
fc["HI"][:] = (0.65 - 4.9e-4 * metallicity[i] -
2.9e-4 * metallicity[i]) * fc["density"]
fc["HeI"][:] = tiny_number * fc["density"]
fc["HeII"][:] = tiny_number * fc["density"]
fc["HeIII"][:] = tiny_number * fc["density"]
if my_chemistry.primordial_chemistry > 1:
fc["H2I"][:] = 0.30 * fc["density"]
fc["H2II"][:] = tiny_number * fc["density"]
fc["HM"][:] = tiny_number * fc["density"]
if my_chemistry.primordial_chemistry > 2:
fc["HDI"][:] = 1.e-9 * fc["density"]
fc["DI"][:] = (3.e-5 - fc["HDI"][:]) * fc["density"]
fc["DII"][:] = tiny_number * fc["density"]
my_chemistry.a_units
my_chemistry.density_units = mass_hydrogen_cgs # rho = 1.0 is 1.67e-24 g
my_chemistry.length_units = cm_per_mpc # 1 Mpc in cm
my_chemistry.time_units = sec_per_Myr # 1 Myr in s
my_chemistry.set_velocity_units()
# set initial density and temperature
initial_temperature = 50000. # start the gas at this temperature
# then begin collapse
initial_density = 1.0e-1 * mass_hydrogen_cgs # g / cm^3
# stopping condition
final_density = 1.e12 * mass_hydrogen_cgs
rval = my_chemistry.initialize()
fc = FluidContainer(my_chemistry, 1)
fc["density"][:] = initial_density / my_chemistry.density_units
fc["HI"][:] = 0.76 * fc["density"]
fc["HII"][:] = tiny_number * 0.76 * fc["density"]
fc["HeI"][:] = (1.0 - 0.76) * fc["density"]
fc["HeII"][:] = tiny_number * fc["density"]
fc["HeIII"][:] = tiny_number * fc["density"]
fc["de"][:] = 2e-4 * mass_electron_cgs / mass_hydrogen_cgs * fc["density"]
if my_chemistry.primordial_chemistry > 1:
fc["H2I"][:] = tiny_number * fc["density"]
fc["H2II"][:] = tiny_number * fc["density"]
fc["HM"][:] = tiny_number * fc["density"]
if my_chemistry.primordial_chemistry > 2:
fc["DI"][:] = 2.0 * 3.4e-5 * fc["density"]
fc["DII"][:] = tiny_number * fc["density"]
fc["HDI"][:] = tiny_number * fc["density"]
# Set units
my_chemistry.comoving_coordinates = 0 # proper units
my_chemistry.a_units = 1.0
my_chemistry.a_value = 1. / (1. + current_redshift) / \
my_chemistry.a_units
my_chemistry.density_units = mass_hydrogen_cgs # rho = 1.0 is 1.67e-24 g
my_chemistry.length_units = cm_per_mpc # 1 Mpc in cm
my_chemistry.time_units = sec_per_Myr # 1 Myr in s
my_chemistry.velocity_units = my_chemistry.a_units * \
(my_chemistry.length_units / my_chemistry.a_value) / \
my_chemistry.time_units
rval = my_chemistry.initialize()
fc = FluidContainer(my_chemistry, 1)
fc["density"][:] = density
if my_chemistry.primordial_chemistry > 0:
fc["HI"][:] = 0.76 * fc["density"]
fc["HII"][:] = tiny_number * fc["density"]
fc["HeI"][:] = (1.0 - 0.76) * fc["density"]
fc["HeII"][:] = tiny_number * fc["density"]
fc["HeIII"][:] = tiny_number * fc["density"]
if my_chemistry.primordial_chemistry > 1:
fc["H2I"][:] = tiny_number * fc["density"]
fc["H2II"][:] = tiny_number * fc["density"]
fc["HM"][:] = tiny_number * fc["density"]
fc["de"][:] = tiny_number * fc["density"]
if my_chemistry.primordial_chemistry > 2:
fc["DI"][:] = 2.0 * 3.4e-5 * fc["density"]
fc["DII"][:] = tiny_number * fc["density"]
def _calculate_cooling_metallicity(field, data, fc):
gfields = _get_needed_fields(fc.chemistry_data)
if field.name[1].endswith('tdt'):
tdfield = 'total_dynamical_time'
else:
tdfield = 'dynamical_time'
td = data['gas', tdfield].to('code_time').d
flatten = len(td.shape) > 1
if flatten:
td = td.flatten()
fc_mini = FluidContainer(data.ds.grackle_data, 1)
fc.calculate_cooling_time()
def cdrat(Z, my_td):
fc_mini['metal'][:] = Z * fc_mini['density']
fc_mini.calculate_cooling_time()
return my_td + fc_mini['cooling_time'][0]
field_data = data.ds.arr(np.zeros(td.size), '')
if isinstance(data, FieldDetector):
return field_data
if field_data.size > 200000:
my_str = "Reticulating splines"
if ytcfg.getboolean("yt", "__parallel"):
my_str = "P%03d %s" % \
(ytcfg.getint("yt", "__global_parallel_rank"),
my_str)
pbar = get_pbar(my_str, field_data.size, parallel=True)
else:
pbar = DummyProgressBar()
for i in range(field_data.size):
pbar.update(i)
if td[i] + fc['cooling_time'][i] > 0:
continue
for mfield in gfields:
fc_mini[mfield][:] = fc[mfield][i]
success = False
if i > 0 and field_data[i - 1] > 0:
try:
field_data[i] = brentq(cdrat,
0.1 * field_data[i - 1],
10 * field_data[i - 1],
args=(td[i]),
xtol=1e-6)
success = True
except:
pass
if not success:
bds = np.logspace(-2, 2, 5)
for bd in bds:
try:
field_data[i] = brentq(cdrat,
1e-6,
bd,
args=(td[i]),
xtol=1e-6)
success = True
break
except:
continue
if not success:
field_data[i] = np.nan
# field_data[i] = 0. # hack for imaging
pbar.finish()
if flatten:
field_data = field_data.reshape(data.ActiveDimensions)
return field_data
def run_grackle(initial_temperature, density, final_time, safety_factor=1e-2):
current_redshift = 0.
tiny_number = 1.0e-20
pygrackle.evolve_constant_density = _new_evolve_constant_density
# Set solver parameters
my_chemistry = chemistry_data()
my_chemistry.three_body_rate = 4
my_chemistry.use_grackle = 1
my_chemistry.with_radiative_cooling = 0
my_chemistry.primordial_chemistry = 2
my_chemistry.metal_cooling = 0
my_chemistry.UVbackground = 0
my_chemistry.self_shielding_method = 0
my_chemistry.H2_self_shielding = 0
grackle_dir = os.path.dirname(
os.path.dirname(
os.path.dirname(os.path.dirname(os.path.abspath(__file__)))))
my_chemistry.grackle_data_file = os.sep.join(
[grackle_dir, "input", "CloudyData_UVB=HM2012.h5"])
# Set units
my_chemistry.comoving_coordinates = 0 # proper units
my_chemistry.a_units = 1.0
my_chemistry.three_body_rate = 4
my_chemistry.a_value = 1. / (1. + current_redshift) / \
my_chemistry.a_units
my_chemistry.density_units = 1.66053904e-24 # 1u: amu # rho = 1.0 is 1.67e-24 g
my_chemistry.length_units = 1.0 # cm
my_chemistry.time_units = 1.0 # s
my_chemistry.velocity_units = my_chemistry.a_units * \
(my_chemistry.length_units / my_chemistry.a_value) / \
my_chemistry.time_units
rval = my_chemistry.initialize()
fc = FluidContainer(my_chemistry, 1)
fc["density"][:] = density
tiny_number = 1.0e-20
if my_chemistry.primordial_chemistry > 0:
# these are in mass_density
fc["HI"][:] = 0.76 * fc["density"] / 3.
fc["HII"][:] = 0.76 * fc["density"] / 3.
fc["HeI"][:] = (1 - 0.76) * fc["density"] / 2.
fc["HeII"][:] = (1 - 0.76) * fc["density"] / 2.
fc["HeIII"][:] = tiny_number
if my_chemistry.primordial_chemistry > 1:
fc["H2I"][:] = 0.76 * fc["density"] / 3.
fc["H2II"][:] = tiny_number #0.76 * fc["density"] /4.
fc["HM"][:] = tiny_number #0.76 * fc["density"] /4.
if my_chemistry.primordial_chemistry > 2:
fc["DI"][:] = 2.0 * 3.4e-5 * fc["density"]
fc["DII"][:] = tiny_number * fc["density"]
fc["HDI"][:] = tiny_number * fc["density"]
if my_chemistry.metal_cooling == 1:
fc["metal"][:] = 0.1 * fc["density"] * \
my_chemistry.SolarMetalFractionByMass
fc["x-velocity"][:] = 0.0
fc["y-velocity"][:] = 0.0
fc["z-velocity"][:] = 0.0
fc["energy"][:] = initial_temperature / \
fc.chemistry_data.temperature_units
fc.calculate_temperature()
fc["energy"][:] *= initial_temperature / fc["temperature"]
# let gas cool at constant density
data = pygrackle.evolve_constant_density(fc,
final_time=final_time,
safety_factor=safety_factor)
return data
my_chemistry.time_units = sec_per_Myr # 1 Myr in s
my_chemistry.velocity_units = my_chemistry.a_units * \
(my_chemistry.length_units / my_chemistry.a_value) / \
my_chemistry.time_units
# set initial density and temperature
initial_temperature = 300.
#initial_temperature = 40000. # start the gas at this temperature
# then begin collapse
initial_density = 1.e-1 * mass_hydrogen_cgs # g / cm^3
# stopping condition
final_density = 1.e10 * mass_hydrogen_cgs
rval = my_chemistry.initialize()
fc = FluidContainer(my_chemistry, 1)
fc["density"][:] = initial_density / my_chemistry.density_units
fc["HII"][:] = 1.e-4 * fc["density"]
fc["HeI"][:] = 8.333e-2 * fc["density"]
fc["HeII"][:] = tiny_number * fc["density"]
fc["HeIII"][:] = tiny_number * fc["density"]
if my_chemistry.primordial_chemistry > 1:
fc["H2I"][:] = 1.e-6 * fc["density"]
fc["H2II"][:] = tiny_number * fc["density"]
fc["HM"][:] = tiny_number * fc["density"]
if my_chemistry.primordial_chemistry > 2:
fc["HDI"][:] = 1.e-9 * fc["density"]
fc["DI"][:] = (3.e-5 - fc["HDI"][:]) * fc["density"]
fc["DII"][:] = tiny_number * fc["density"]
if my_chemistry.metal_cooling == 1:
fc["metal"][:] = metallicity[i] * my_chemistry.SolarMetalFractionByMass * \
def run_grackle(density = 1e10, initial_temperature = 1e3, final_time = 1e5, safety_factor=1e-2):
current_redshift = 0.
tiny_number = 1.0e-20
pygrackle.evolve_constant_density = _new_evolve_constant_density
# Set solver parameters
my_chemistry = chemistry_data()
my_chemistry.three_body_rate = 4
my_chemistry.use_grackle = 1
my_chemistry.with_radiative_cooling = 1
my_chemistry.primordial_chemistry = 2
my_chemistry.metal_cooling = 0
my_chemistry.UVbackground = 0
my_chemistry.self_shielding_method = 0
my_chemistry.H2_self_shielding = 0
my_chemistry.cie_cooling = 0
grackle_dir = "/home/kwoksun2/grackle"
my_chemistry.grackle_data_file = os.sep.join(
[grackle_dir, "input", "CloudyData_UVB=HM2012.h5"])
# Set units
my_chemistry.comoving_coordinates = 0 # proper units
my_chemistry.a_units = 1.0
my_chemistry.three_body_rate = 4
my_chemistry.a_value = 1. / (1. + current_redshift) / \
my_chemistry.a_units
my_chemistry.density_units = 1.66053904e-24 # 1u: amu # rho = 1.0 is 1.67e-24 g
my_chemistry.length_units = 1.0 # cm
my_chemistry.time_units = 1.0 # s
my_chemistry.velocity_units = my_chemistry.a_units * \
(my_chemistry.length_units / my_chemistry.a_value) / \
my_chemistry.time_units
rval = my_chemistry.initialize()
fc = FluidContainer(my_chemistry, 1)
fc["density"][:] = density
tiny_number = 1.0e-20
if my_chemistry.primordial_chemistry > 0:
# these are in mass_density
fc["HI"][:] = 0.76 * fc["density"] /3.
fc["HII"][:] = 0.76 * fc["density"] /3.
fc["HeI"][:] = (1 - 0.76) * fc["density"] /2.
fc["HeII"][:] = (1 - 0.76) * fc["density"] /2.
fc["HeIII"][:] = tiny_number
if my_chemistry.primordial_chemistry > 1:
fc["H2I"][:] = 0.76 * fc["density"] /3.
fc["H2II"][:] = tiny_number
fc["HM"][:] = tiny_number
fc["de"][:] = fc["HII"][:] + fc["HeII"][:]/4. + fc["HeIII"][:]/4.*2.0
if my_chemistry.primordial_chemistry > 2:
fc["DI"][:] = 2.0 * 3.4e-5 * fc["density"]
fc["DII"][:] = tiny_number * fc["density"]
fc["HDI"][:] = tiny_number * fc["density"]
if my_chemistry.metal_cooling == 1:
fc["metal"][:] = 0.1 * fc["density"] * \
my_chemistry.SolarMetalFractionByMass
fc["x-velocity"][:] = 0.0
fc["y-velocity"][:] = 0.0
fc["z-velocity"][:] = 0.0
fc["energy"][:] = initial_temperature / \
fc.chemistry_data.temperature_units
fc.calculate_temperature()
fc["energy"][:] *= initial_temperature / fc["temperature"]
tic = timeit.default_timer()
# let gas cool at constant density
data = pygrackle.evolve_constant_density(
fc, final_time=final_time,
safety_factor=safety_factor)
toc = timeit.default_timer()
run_time = toc - tic
print("time lapsed", run_time)
# convert grackle language to dengo language
name_map_dict = { 'HI':'H_1',
'HII':'H_2',
'HeI':'He_1',
'HeII':'He_2',
'HeIII':'He_3',
'H2I' : 'H2_1',
'H2II': 'H2_2',
'HM' : 'H_m0',
'de':'de',
'temperature':'T',
'time': 't',
'energy':'ge'}
weight_map_dict = { 'HI':1.00794,
'HII':1.00794,
'HeI':4.002602,
'HeII':4.002602,
'HeIII':4.002602,
'H2II': 2.01588,
'H2I' : 2.01588,
'HM' : 1.00794,
'de':1.00794,
'time': 1.0,
'temperature': 1.0,
'energy': 1.0}
data_grackle = {}
for key in name_map_dict.keys():
key_dengo = name_map_dict[key]
if key_dengo in ["t","T","ge"]:
data_grackle[key_dengo] = data[key].value
else:
data_grackle[key_dengo] = data[key].value / weight_map_dict[key] / u.amu_cgs.value
save_obj(data_grackle, 'grackle_data')
return data_grackle, run_time
my_chemistry.velocity_units = my_chemistry.a_units * \
(my_chemistry.length_units / my_chemistry.a_value) / \
my_chemistry.time_units
# self-shielding cross sections in CGS
my_chemistry.hi_pi_avg_cross_section = 2.49E-18
my_chemistry.hi_ph_avg_cross_section = 2.49E-18
my_chemistry.hei_ph_avg_cross_section = 4.1294e-18
my_chemistry.hei_pi_avg_cross_section = 4.1294e-18
my_chemistry.heii_ph_avg_cross_section = 0.0
my_chemistry.heii_pi_avg_cross_section = 0.0
rval = my_chemistry.initialize()
fc = FluidContainer(my_chemistry, 1)
fc["density"][:] = density
if my_chemistry.primordial_chemistry > 0:
fc["HI"][:] = 0.76 * fc["density"]
fc["HII"][:] = tiny_number * fc["density"]
fc["HeI"][:] = (1.0 - 0.76) * fc["density"]
fc["HeII"][:] = tiny_number * fc["density"]
fc["HeIII"][:] = tiny_number * fc["density"]
if my_chemistry.primordial_chemistry > 1:
fc["H2I"][:] = tiny_number * fc["density"]
fc["H2II"][:] = tiny_number * fc["density"]
fc["HM"][:] = tiny_number * fc["density"]
fc["de"][:] = tiny_number * fc["density"]
if my_chemistry.primordial_chemistry > 2:
fc["DI"][:] = 2.0 * 3.4e-5 * fc["density"]
fc["DII"][:] = tiny_number * fc["density"]
my_chemistry.density_units = mass_hydrogen_cgs # rho = 1.0 is 1.67e-24 g
my_chemistry.length_units = cm_per_mpc # 1 Mpc in cm
my_chemistry.time_units = sec_per_Myr # 1 Myr in s
my_chemistry.velocity_units = my_chemistry.a_units * \
(my_chemistry.length_units / my_chemistry.a_value) / \
my_chemistry.time_units
# set initial density and temperature
initial_temperature = 100.
#initial_density = 1.0e3/0.9 * mass_hydrogen_cgs
initial_density = 1.e3 * mass_hydrogen_cgs
final_time = 3.2e3 # 0.05 #1.e3 #1. # 1.e3 # 1.e3 # in Myr
rval = my_chemistry.initialize()
fc = FluidContainer(my_chemistry, 1)
fc["density"][:] = initial_density / my_chemistry.density_units
fc["HII"][:] = tiny_number * fc["density"]
fc["HI"][:] = (0.65 - 4.9e-4 * metallicity[i] - 2.9e-4 * metallicity[i])* fc["density"]
fc["HeI"][:] = tiny_number * fc["density"]
fc["HeII"][:] = tiny_number * fc["density"]
fc["HeIII"][:] = tiny_number * fc["density"]
if my_chemistry.primordial_chemistry > 1:
fc["H2I"][:] = 0.30 * fc["density"]
fc["H2II"][:] = tiny_number * fc["density"]
fc["HM"][:] = tiny_number * fc["density"]
if my_chemistry.primordial_chemistry > 2:
fc["HDI"][:] = 1.e-9 * fc["density"]
fc["DI"][:] = (3.e-5 - fc["HDI"][:]) * fc["density"]
fc["DII"][:] = tiny_number * fc["density"]
if my_chemistry.metal_cooling == 1:
def cooling_cell(density=12.2,
initial_temperature=2.0E4,
final_time=30.0,
metal_fraction=4.0E-4,
make_plot=False,
save_output=False,
primordial_chemistry=2,
outname=None,
save_H2_fraction=False,
return_result=False,
verbose=False,
H2_converge=None,
*args,
**kwargs):
current_redshift = 0.
# Set solver parameters
my_chemistry = chemistry_data()
my_chemistry.use_grackle = 1
my_chemistry.with_radiative_cooling = 1
my_chemistry.primordial_chemistry = primordial_chemistry
my_chemistry.metal_cooling = 1
my_chemistry.UVbackground = 1
my_chemistry.self_shielding_method = 3
if primordial_chemistry > 1:
my_chemistry.H2_self_shielding = 2
my_chemistry.h2_on_dust = 1
my_chemistry.three_body_rate = 4
grackle_dir = "/home/aemerick/code/grackle-emerick/"
my_chemistry.grackle_data_file = os.sep.join( #['/home/aemerick/code/grackle-emerick/input/CloudyData_UVB=HM2012.h5'])
[grackle_dir, "input", "CloudyData_UVB=HM2012_shielded.h5"])
# set the factors
my_chemistry.LW_factor = kwargs.get("LW_factor", 1.0)
my_chemistry.k27_factor = kwargs.get("k27_factor", 1.0)
#if 'LW_factor' in kwargs.keys():
# my_chemistry.LW_factor = kwargs['LW_factor']
#else:
# my_chemistry.LW_factor = 1.0
#if 'k27_factor' in kwargs.keys():
# my_chemistry.k27_factor = kwargs['k27_factor']
#else:
# my_chemistry.k27_factor = 1.0
# Set units
my_chemistry.comoving_coordinates = 0 # proper units
my_chemistry.a_units = 1.0
my_chemistry.a_value = 1. / (1. + current_redshift) / \
my_chemistry.a_units
my_chemistry.density_units = mass_hydrogen_cgs # rho = 1.0 is 1.67e-24 g
my_chemistry.length_units = cm_per_mpc # 1 Mpc in cm
my_chemistry.time_units = sec_per_Myr # 1 Myr in s
my_chemistry.velocity_units = my_chemistry.a_units * \
(my_chemistry.length_units / my_chemistry.a_value) / \
my_chemistry.time_units
rval = my_chemistry.initialize()
fc = FluidContainer(my_chemistry, 1)
fc["density"][:] = density
if my_chemistry.primordial_chemistry > 0:
fc["HI"][:] = 0.76 * fc["density"]
fc["HII"][:] = tiny_number * fc["density"]
fc["HeI"][:] = (1.0 - 0.76) * fc["density"]
fc["HeII"][:] = tiny_number * fc["density"]
fc["HeIII"][:] = tiny_number * fc["density"]
if my_chemistry.primordial_chemistry > 1:
fc["H2I"][:] = tiny_number * fc["density"]
fc["H2II"][:] = tiny_number * fc["density"]
fc["HM"][:] = tiny_number * fc["density"]
fc["de"][:] = tiny_number * fc["density"]
fc['H2_self_shielding_length'][:] = 1.8E-6
if my_chemistry.primordial_chemistry > 2:
fc["DI"][:] = 2.0 * 3.4e-5 * fc["density"]
fc["DII"][:] = tiny_number * fc["density"]
fc["HDI"][:] = tiny_number * fc["density"]
if my_chemistry.metal_cooling == 1:
fc["metal"][:] = metal_fraction * fc["density"] * \
my_chemistry.SolarMetalFractionByMass
fc["x-velocity"][:] = 0.0
fc["y-velocity"][:] = 0.0
fc["z-velocity"][:] = 0.0
fc["energy"][:] = initial_temperature / \
fc.chemistry_data.temperature_units
fc.calculate_temperature()
fc["energy"][:] *= initial_temperature / fc["temperature"]
# timestepping safety factor
safety_factor = 0.001
# let gas cool at constant density
#if verbose:
print("Beginning Run")
data = evolve_constant_density(fc,
final_time=final_time,
H2_converge=H2_converge,
safety_factor=safety_factor,
verbose=verbose)
#else:
# print "Beginning Run"
# with NoStdStreams():
# data = evolve_constant_density(
# fc, final_time=final_time, H2_converge = 1.0E-6,
# safety_factor=safety_factor)
# print "Ending Run"
if make_plot:
p1, = plt.loglog(data["time"].to("Myr"),
data["temperature"],
color="black",
label="T")
plt.xlabel("Time [Myr]")
plt.ylabel("T [K]")
data["mu"] = data["temperature"] / \
(data["energy"] * (my_chemistry.Gamma - 1.) *
fc.chemistry_data.temperature_units)
plt.twinx()
p2, = plt.semilogx(data["time"].to("Myr"),
data["mu"],
color="red",
label="$\\mu$")
plt.ylabel("$\\mu$")
plt.legend([p1, p2], ["T", "$\\mu$"], fancybox=True, loc="center left")
plt.savefig("cooling_cell.png")
# save data arrays as a yt dataset
if outname is None:
outname = 'cooling_cell_%.2f_%.2f' % (my_chemistry.k27_factor,
my_chemistry.LW_factor)
if save_output:
yt.save_as_dataset({}, outname + '.h5', data)
if my_chemistry.primordial_chemistry > 1:
H2_fraction = (data['H2I'] + data['H2II']) / data['density']
else:
H2_fraction = np.zeros(np.size(data['density']))
if save_H2_fraction:
#np.savetxt(outname + ".dat", [data['time'], H2_fraction])
f = open("all_runs_d_%.2f.dat" % (density), "a")
# f.write("# k27 LW f_H2 T time\n")
f.write("%8.8E %8.8E %8.8E %8.8E %8.8E \n" %
(my_chemistry.k27_factor, my_chemistry.LW_factor,
H2_fraction[-1], data['temperature'][-1], data['time'][-1]))
f.close()
if return_result:
return data
else:
return