zh2 = 2.8
mu_h2 = yt.YTArray(zh2 * u.Da.to(u.g), 'g')
# Problem setup: pure density field
sz = 16
max_rad = 10000 * u.au
rbreak = 1000 * u.au
zz, yy, xx = np.indices([sz, sz, sz]) * max_rad / (sz / 2.)
mid = max_rad * (sz - 1.) / sz
rr = ((zz - mid)**2 + (yy - mid)**2 + (xx - mid)**2)**0.5
max_velo = 2 * u.km / u.s
velo = max_velo - u.Quantity([mid - zz, mid - yy, mid - xx
]) / rr.max() * max_velo
# now rr has units
dens = broken_powerlaw(rr, rbreak=rbreak, n0=5e8 * u.cm**-3, power=-1.5)
data = {
'density': ((dens * u.Da * zh2).to(u.g / u.cm**3), "g/cm**3"),
'z_velocity': (velo[0].to(u.km / u.s).value, 'km/s'),
'y_velocity': (velo[1].to(u.km / u.s).value, 'km/s'),
'x_velocity': (velo[2].to(u.km / u.s).value, 'km/s'),
}
bbox = np.array([[-max_rad.value, max_rad.value]] * 3)
ds = yt.load_uniform_grid(data,
dens.shape,
length_unit="au",
bbox=bbox,
nprocs=64)
dust_to_gas = 0.01
zh2 = 2.8
mu_h2 = yt.YTArray(zh2 * u.Da.to(u.g), 'g')
# Problem setup: pure density field
sz = 16
max_rad = 10000*u.au
rbreak = 1000*u.au
zz,yy,xx = np.indices([sz,sz,sz]) * max_rad / (sz/2.)
mid = max_rad * (sz-1.)/sz
rr = ((zz-mid)**2 + (yy-mid)**2 + (xx-mid)**2)**0.5
max_velo = 2*u.km/u.s
velo = max_velo - u.Quantity([mid-zz, mid-yy, mid-xx]) / rr.max() * max_velo
# now rr has units
dens = broken_powerlaw(rr, rbreak=rbreak, n0=5e8*u.cm**-3, power=-1.5)
data = {'density': ((dens*u.Da*zh2).to(u.g/u.cm**3), "g/cm**3"),
'z_velocity': (velo[0].to(u.km/u.s).value, 'km/s'),
'y_velocity': (velo[1].to(u.km/u.s).value, 'km/s'),
'x_velocity': (velo[2].to(u.km/u.s).value, 'km/s'),
}
bbox = np.array([[-max_rad.value,max_rad.value]]*3)
ds = yt.load_uniform_grid(data, dens.shape, length_unit="au", bbox=bbox, nprocs=64)
dust_to_gas = 0.01
def _DustDensity(field, data):
return dust_to_gas * data['density']
ds.add_field(("gas", "dust_density"), function=_DustDensity, units="g/cm**3")
def _NumberDensityCH3OH(field, data):
def core_model_dust(outname, x_co=1.0e-4, x_h2co=1.0e-9, x_ch3oh=1e-9, zh2=2.8,
sz=16, max_rad=10000*u.au, rbreak=1000*u.au,
radius_cm=1*u.au.to(u.cm), mass_g=1*u.M_sun.to(u.g),
n0=5e8*u.cm**-3,
power=-1.5,
recompute_dusttemperature=True,
luminosity=2e4*u.L_sun,):
if not os.path.exists('dustkappa_mrn5.inp'):
get_dust_opacity()
mu_h2 = yt.YTArray(zh2 * u.Da.to(u.g), 'g')
# Problem setup: pure density field
zz,yy,xx = np.indices([sz,sz,sz])
rr = ((zz-(sz-1)/2.)**2 + (yy-(sz-1)/2.)**2 + (xx-(sz-1)/2.)**2)**0.5
max_velo = 1*u.km/u.s
velo = max_velo - np.array([(sz-1)/2.-zz, (sz-1/2.)-yy, (sz-1/2.)-xx]) / rr.max() * max_velo
# now rr has units
rr = rr * max_rad / (sz/2.)
dens = broken_powerlaw(rr, rbreak=rbreak, n0=n0, power=power)
data = {('gas','density'): ((dens*u.Da*zh2).to(u.g/u.cm**3), "g/cm**3"),
('gas','z_velocity'): (velo[0].to(u.km/u.s).value, 'km/s'),
('gas','y_velocity'): (velo[1].to(u.km/u.s).value, 'km/s'),
('gas','x_velocity'): (velo[2].to(u.km/u.s).value, 'km/s'),
}
bbox = np.array([[-max_rad.value,max_rad.value]]*3)
ds = yt.load_uniform_grid(data, dens.shape, length_unit="au", bbox=bbox, nprocs=64)
dust_to_gas = 0.01
def _DustDensity(field, data):
return dust_to_gas * data['density']
ds.add_field(("gas", "dust_density"), function=_DustDensity, units="g/cm**3")
def _NumberDensityH2(field, data):
return (1./mu_h2)*data['density'] # data['density']#
ds.add_field(("gas", "number_density_H2"), function=_NumberDensityH2, units="cm**-3")
def _GasTemperature(field, data):
return yt.YTArray(np.ones_like(data['density'])*100., 'K')
ds.add_field(("gas", "temperature"), function=_GasTemperature, units='K')
def _DustTemperature(field, data):
return yt.YTArray(np.ones_like(data['density'])*100., 'K')
ds.add_field(("gas", "dust_temperature"), function=_DustTemperature, units='K')
writer = RadMC3DWriter(ds)
writer.write_amr_grid()
dens_fn = "numberdens_h2.inp" # not h2_numberdens.inp?
writer.write_line_file(("gas", "number_density_H2"), dens_fn)
writer.write_dust_file(("gas", "temperature"), "gas_temperature.inp")
writer.write_dust_file(("gas", "dust_density"), "dust_density.inp")
#writer.write_dust_file(("gas", "dust_temperature"), "dust_temperature.inp")
writer.write_line_file([('gas','x_velocity'), ('gas','y_velocity'),
('gas','z_velocity')], "gas_velocity.inp")
# central star
position_cm = [0.0, 0.0, 0.0]
temperature_K = 1000.0
temperature_K = ((luminosity /
(4 * np.pi * (radius_cm*u.cm)**2 * constants.sigma_sb))**0.25
).to(u.K).value
star = RadMC3DSource(radius_cm, mass_g, position_cm, temperature_K)
sources_list = [star]
wavelengths_micron = np.logspace(-1.0, 4.0, 1000)
writer.write_source_files(sources_list, wavelengths_micron)
get_dust_opacity()
params=dict(istar_sphere=0, itempdecoup=0, lines_mode=3, nphot=1000000,
nphot_scat=30000, nphot_spec=100000, rto_style=3,
scattering_mode=0, scattering_mode_max=0, tgas_eq_tdust=1,)
params_string = """
istar_sphere = {istar_sphere}
itempdecoup = {itempdecoup}
lines_mode = {lines_mode}
nphot = {nphot}
nphot_scat = {nphot_scat}
nphot_spec = {nphot_spec}
rto_style = {rto_style}
scattering_mode = {scattering_mode}
scattering_mode_max = {scattering_mode_max}
tgas_eq_tdust = {tgas_eq_tdust}
"""
with open('wavelength_micron.inp', 'w') as fh:
fh.write("{0}\n".format(len(wavelengths_micron)))
for nu in wavelengths_micron:
fh.write("{0}\n".format(nu))
# with open('stars.inp', 'w') as fh:
# fh.write("2\n")
# nstars = 1
# nlam = nfrq
# fh.write("{0} {1}\n".format(nstars,nlam))
# rstar = (1*u.au).to(u.cm).value
# mstar = 15*u.M_sun.to(u.g)
# x,y,z = 0,0,0
# fh.write("{0} {1} {2} {3} {4}\n".format(rstar, mstar, x, y, z))
# for nu in wavelengths_micron:
# fh.write("{0}\n".format(nu))
# temperature = 1000 * u.K
# for nu in wavelengths_micron:
# fh.write("{0}\n".format(-temperature.to(u.K).value))
with open('radmc3d.inp','w') as f:
params['lines_mode'] = 1 # 3 = sobolev (LVG)
f.write(params_string.format(**params))
if recompute_dusttemperature:
# compute the dust temperature
assert os.system('radmc3d mctherm') == 0
dust_temperature = read_dust_temperature('dust_temperature.bdat', sz=sz)
shutil.copy('dust_temperature.bdat','dust_temperature_{0}.bdat'.format(outname))
else:
try:
shutil.copy('dust_temperature_{0}.bdat'.format(outname),'dust_temperature.bdat',)
except Exception as ex:
print(ex)
dust_temperature = read_dust_temperature('dust_temperature.bdat', sz=sz)
if os.path.exists('lines.inp'):
os.remove('lines.inp')
assert os.system('radmc3d image npix 50 incl 0 sizeau 10000 noscat pointau 0.0 0.0 0.0 fluxcons lambda 1323 dpc 5400') == 0
im = radmc3dPy.image.readImage('image.out')
im.writeFits('dustim1323um_{0}.fits'.format(outname), fitsheadkeys={}, dpc=5400,
coord='19h23m43.963s +14d30m34.56s', overwrite=True)
return dust_temperature
def core_model_dust(
outname,
x_co=1.0e-4,
x_h2co=1.0e-9,
x_ch3oh=1e-9,
zh2=2.8,
sz=16,
max_rad=10000 * u.au,
rbreak=1000 * u.au,
radius_cm=1 * u.au.to(u.cm),
mass_g=1 * u.M_sun.to(u.g),
n0=5e8 * u.cm**-3,
power=-1.5,
recompute_dusttemperature=True,
luminosity=2e4 * u.L_sun,
):
if not os.path.exists('dustkappa_mrn5.inp'):
get_dust_opacity()
mu_h2 = yt.YTArray(zh2 * u.Da.to(u.g), 'g')
# Problem setup: pure density field
zz, yy, xx = np.indices([sz, sz, sz])
rr = ((zz - (sz - 1) / 2.)**2 + (yy - (sz - 1) / 2.)**2 +
(xx - (sz - 1) / 2.)**2)**0.5
max_velo = 1 * u.km / u.s
velo = max_velo - np.array([(sz - 1) / 2. - zz, (sz - 1 / 2.) - yy,
(sz - 1 / 2.) - xx]) / rr.max() * max_velo
# now rr has units
rr = rr * max_rad / (sz / 2.)
dens = broken_powerlaw(rr, rbreak=rbreak, n0=n0, power=power)
data = {
('gas', 'density'): ((dens * u.Da * zh2).to(u.g / u.cm**3), "g/cm**3"),
('gas', 'z_velocity'): (velo[0].to(u.km / u.s).value, 'km/s'),
('gas', 'y_velocity'): (velo[1].to(u.km / u.s).value, 'km/s'),
('gas', 'x_velocity'): (velo[2].to(u.km / u.s).value, 'km/s'),
}
bbox = np.array([[-max_rad.value, max_rad.value]] * 3)
ds = yt.load_uniform_grid(data,
dens.shape,
length_unit="au",
bbox=bbox,
nprocs=64)
dust_to_gas = 0.01
def _DustDensity(field, data):
return dust_to_gas * data['density']
ds.add_field(("gas", "dust_density"),
function=_DustDensity,
units="g/cm**3")
def _NumberDensityH2(field, data):
return (1. / mu_h2) * data['density'] # data['density']#
ds.add_field(("gas", "number_density_H2"),
function=_NumberDensityH2,
units="cm**-3")
def _GasTemperature(field, data):
return yt.YTArray(np.ones_like(data['density']) * 100., 'K')
ds.add_field(("gas", "temperature"), function=_GasTemperature, units='K')
def _DustTemperature(field, data):
return yt.YTArray(np.ones_like(data['density']) * 100., 'K')
ds.add_field(("gas", "dust_temperature"),
function=_DustTemperature,
units='K')
writer = RadMC3DWriter(ds)
writer.write_amr_grid()
dens_fn = "numberdens_h2.inp" # not h2_numberdens.inp?
writer.write_line_file(("gas", "number_density_H2"), dens_fn)
writer.write_dust_file(("gas", "temperature"), "gas_temperature.inp")
writer.write_dust_file(("gas", "dust_density"), "dust_density.inp")
#writer.write_dust_file(("gas", "dust_temperature"), "dust_temperature.inp")
writer.write_line_file([('gas', 'x_velocity'), ('gas', 'y_velocity'),
('gas', 'z_velocity')], "gas_velocity.inp")
# central star
position_cm = [0.0, 0.0, 0.0]
temperature_K = 1000.0
temperature_K = ((luminosity /
(4 * np.pi *
(radius_cm * u.cm)**2 * constants.sigma_sb))**0.25).to(
u.K).value
star = RadMC3DSource(radius_cm, mass_g, position_cm, temperature_K)
sources_list = [star]
wavelengths_micron = np.logspace(-1.0, 4.0, 1000)
writer.write_source_files(sources_list, wavelengths_micron)
get_dust_opacity()
params = dict(
istar_sphere=0,
itempdecoup=0,
lines_mode=3,
nphot=10000,
nphot_scat=3000,
nphot_spec=10000,
rto_style=3,
scattering_mode=0,
scattering_mode_max=0,
tgas_eq_tdust=1,
)
params_string = """
istar_sphere = {istar_sphere}
itempdecoup = {itempdecoup}
lines_mode = {lines_mode}
nphot = {nphot}
nphot_scat = {nphot_scat}
nphot_spec = {nphot_spec}
rto_style = {rto_style}
scattering_mode = {scattering_mode}
scattering_mode_max = {scattering_mode_max}
tgas_eq_tdust = {tgas_eq_tdust}
"""
with open('wavelength_micron.inp', 'w') as fh:
fh.write("{0}\n".format(len(wavelengths_micron)))
for nu in wavelengths_micron:
fh.write("{0}\n".format(nu))
# with open('stars.inp', 'w') as fh:
# fh.write("2\n")
# nstars = 1
# nlam = nfrq
# fh.write("{0} {1}\n".format(nstars,nlam))
# rstar = (1*u.au).to(u.cm).value
# mstar = 15*u.M_sun.to(u.g)
# x,y,z = 0,0,0
# fh.write("{0} {1} {2} {3} {4}\n".format(rstar, mstar, x, y, z))
# for nu in wavelengths_micron:
# fh.write("{0}\n".format(nu))
# temperature = 1000 * u.K
# for nu in wavelengths_micron:
# fh.write("{0}\n".format(-temperature.to(u.K).value))
with open('radmc3d.inp', 'w') as f:
params['lines_mode'] = 1 # 3 = sobolev (LVG)
f.write(params_string.format(**params))
if recompute_dusttemperature:
# compute the dust temperature
assert os.system('radmc3d mctherm') == 0
dust_temperature = read_dust_temperature('dust_temperature.bdat',
sz=sz)
shutil.move('dust_temperature.bdat',
'dust_temperature_{0}.bdat'.format(outname))
else:
try:
shutil.copy(
'dust_temperature_{0}.bdat'.format(outname),
'dust_temperature.bdat',
)
success = True
except Exception as ex:
success = False
print(ex)
dust_temperature = read_dust_temperature('dust_temperature.bdat',
sz=sz)
if success:
os.remove('dust_temperature.bdat')
if os.path.exists('lines.inp'):
os.remove('lines.inp')
assert os.system(
'radmc3d image npix 50 incl 0 sizeau 10000 noscat pointau 0.0 0.0 0.0 fluxcons lambda 1323 dpc 5400'
) == 0
im = radmc3dPy.image.readImage('image.out')
im.writeFits('dustim1323um_{0}.fits'.format(outname),
fitsheadkeys={},
dpc=5400,
coord='19h23m43.963s +14d30m34.56s',
overwrite=True)
return dust_temperature
