def run_yso_model( Tstar=None, logL_star=None, \
logM_disk=None, logR_disk=None, h_0=None, logR_in=None, gamma=None, \
beta=None, logM_env=None, logR_env=None, f_cav=None, ksi=None, \
loga_max=None, p=None, incl=None):
params = [Tstar,logL_star,logM_disk,logR_disk,h_0,logR_in,\
gamma,beta,logM_env,logR_env,f_cav,ksi,loga_max,p,incl]
param_names = ['Tstar','logLstar','logMdisk','logRdisk','h0','logRin',\
'gamma','beta','logMenv','logRenv','fcav','ksi','logamax','p','incl']
# Set up the dust properties.
dust_gen = dust.DustGenerator(dust.__path__[0] + "/data/diana_wice.hdf5")
ddust = dust_gen(10.**loga_max / 1e4, p)
env_dust_gen = dust.DustGenerator(dust.__path__[0]+\
"/data/diana_wice.hdf5")
edust = env_dust_gen(1.0e-4, 3.5)
# Calculate alpha correctly.
alpha = gamma + beta
# Fix the scale height of the disk.
h_0 *= (10.**logR_disk)**beta
# Set up the model.
model = modeling.YSOModel()
model.add_star(luminosity=10.**logL_star, temperature=Tstar)
model.set_spherical_grid(10.**logR_in, 10.**logR_env, 100, 101, 2, \
code="radmc3d")
model.add_pringle_disk(mass=10.**logM_disk, rmin=10.**logR_in, \
rmax=10.**logR_disk, plrho=alpha, h0=h_0, plh=beta, dust=ddust)
model.add_ulrich_envelope(mass=10.**logM_env, rmin=10.**logR_in, \
rmax=10.**logR_env, cavpl=ksi, cavrfact=f_cav, dust=edust)
model.grid.set_wavelength_grid(0.1, 1.0e5, 500, log=True)
print("finished setting up model, now running thermal simulation")
# Run the thermal simulation
model.run_thermal(code="radmc3d", nphot=1e6, \
modified_random_walk=True, verbose=False, setthreads=17, \
timelimit=10800)
print("finished running thermal simulation, now running SED")
t2 = time()
# Run the SED.
model.set_camera_wavelength(np.logspace(-1., 4., 500))
model.run_sed(name="SED", nphot=1e5, loadlambda=True, incl=incl, \
pa=0., dpc=140., code="radmc3d", camera_scatsrc_allfreq=True, \
verbose=False, setthreads=17)
filename = ""
for i in range(len(param_names)):
filename += param_names[i] + "_"
filename += str(params[i]) + "_"
filename = filename[:-1]
filename += ".hdf5"
print("finished running " + filename[0:40] + "... in %0.3fs" %
(time() - t2))
# Write out the file.
model.write_yso("../../grid/transform/" + filename)
def model(visibilities, params, parameters, plot=False):
# Set the values of all of the parameters.
p = {}
for key in parameters:
if parameters[key]["fixed"]:
if parameters[key]["value"] in parameters.keys():
if parameters[parameters[key]["value"]]["fixed"]:
value = parameters[parameters[key]["value"]]["value"]
else:
value = params[parameters[key]["value"]]
else:
value = parameters[key]["value"]
else:
value = params[key]
if key[0:3] == "log":
p[key[3:]] = 10.**value
else:
p[key] = value
# Make sure alpha and beta are defined.
if p["disk_type"] == "exptaper":
t_rdisk = p["T0"] * (p["R_disk"] / 1.)**-p["q"]
p["h_0"] = ((k_b*(p["R_disk"]*AU)**3*t_rdisk) / (G*p["M_star"]*M_sun * \
2.37*m_p))**0.5 / AU
else:
p["h_0"] = ((k_b * AU**3 * p["T0"]) / (G*p["M_star"]*M_sun * \
2.37*m_p))**0.5 / AU
p["beta"] = 0.5 * (3 - p["q"])
p["alpha"] = p["gamma"] + p["beta"]
# Set up the dust.
dustopac = "pollack_new.hdf5"
dust_gen = dust.DustGenerator(dust.__path__[0] + "/data/" + dustopac)
ddust = dust_gen(p["a_max"] / 1e4, p["p"])
edust = dust_gen(1.0e-4, 3.5)
# Set up the gas.
gases = []
abundance = []
index = 1
while index > 0:
if "gas_file" + str(index) in p:
g = gas.Gas()
g.set_properties_from_lambda(gas.__path__[0]+"/data/"+\
p["gas_file"+str(index)])
gases.append(g)
abundance.append(p["abundance" + str(index)])
index += 1
else:
index = -1
# Make sure we are in a temp directory to not overwrite anything.
original_dir = os.environ["PWD"]
os.mkdir("/tmp/temp_{1:s}_{0:d}".format(comm.Get_rank(), source))
os.chdir("/tmp/temp_{1:s}_{0:d}".format(comm.Get_rank(), source))
# Write the parameters to a text file so it is easy to keep track of them.
f = open("params.txt", "w")
for key in p:
f.write("{0:s} = {1}\n".format(key, p[key]))
f.close()
# Set up the model.
m = modeling.YSOModel()
m.add_star(mass=p["M_star"],
luminosity=p["L_star"],
temperature=p["T_star"])
if p["envelope_type"] == "ulrich":
m.set_spherical_grid(p["R_in"], p["R_env"], 100, 51, 2, code="radmc3d")
else:
m.set_spherical_grid(p["R_in"], max(5*p["R_disk"],300), 100, 51, 2, \
code="radmc3d")
if p["disk_type"] == "exptaper":
m.add_pringle_disk(mass=p["M_disk"], rmin=p["R_in"], rmax=p["R_disk"], \
plrho=p["alpha"], h0=p["h_0"], plh=p["beta"], dust=ddust, \
t0=p["T0"], plt=p["q"], gas=gases, abundance=abundance,\
aturb=p["a_turb"])
else:
m.add_disk(mass=p["M_disk"], rmin=p["R_in"], rmax=p["R_disk"], \
plrho=p["alpha"], h0=p["h_0"], plh=p["beta"], dust=ddust, \
t0=p["T0"], plt=p["q"], gas=gases, abundance=abundance,\
aturb=p["a_turb"])
if p["envelope_type"] == "ulrich":
m.add_ulrich_envelope(mass=p["M_env"], rmin=p["R_in"], rmax=p["R_env"],\
cavpl=p["ksi"], cavrfact=p["f_cav"], dust=edust, \
t0=p["T0_env"], tpl=p["q_env"], gas=gases, abundance=abundance,\
aturb=p["a_turb_env"])
else:
pass
m.grid.set_wavelength_grid(0.1, 1.0e5, 500, log=True)
# Run the images/visibilities/SEDs.
for j in range(len(visibilities["file"])):
# Shift the wavelengths by the velocities.
b = p["v_sys"] * 1.0e5 / c
lam = c / visibilities["data"][j].freq / 1.0e-4
wave = lam * numpy.sqrt((1. - b) / (1. + b))
# Set the wavelengths for RADMC3D to use.
m.set_camera_wavelength(wave)
if p["docontsub"]:
m.run_image(name=visibilities["lam"][j], nphot=1e5, \
npix=visibilities["npix"][j], lam=None, \
pixelsize=visibilities["pixelsize"][j], tgas_eq_tdust=True,\
scattering_mode_max=0, incl_dust=True, incl_lines=True, \
loadlambda=True, incl=p["i"], pa=p["pa"], dpc=p["dpc"], \
code="radmc3d", verbose=False, writeimage_unformatted=True,\
setthreads=ncpus)
m.run_image(name="cont", nphot=1e5, \
npix=visibilities["npix"][j], lam=None, \
pixelsize=visibilities["pixelsize"][j], tgas_eq_tdust=True,\
scattering_mode_max=0, incl_dust=True, incl_lines=False, \
loadlambda=True, incl=p["i"], pa=p["pa"], dpc=p["dpc"], \
code="radmc3d", verbose=False, writeimage_unformatted=True,\
setthreads=ncpus)
m.images[visibilities["lam"][j]].image -= m.images["cont"].image
else:
m.run_image(name=visibilities["lam"][j], nphot=1e5, \
npix=visibilities["npix"][j], lam=None, \
pixelsize=visibilities["pixelsize"][j], tgas_eq_tdust=True,\
scattering_mode_max=0, incl_dust=False, incl_lines=True, \
loadlambda=True, incl=p["i"], pa=p["pa"], dpc=p["dpc"], \
code="radmc3d", verbose=False, writeimage_unformatted=True,\
setthreads=ncpus)
m.visibilities[visibilities["lam"][j]] = uv.interpolate_model(\
visibilities["data"][j].u, visibilities["data"][j].v, \
visibilities["data"][j].freq, \
m.images[visibilities["lam"][j]], dRA=-p["x0"], dDec=-p["y0"], \
nthreads=ncpus)
if plot:
lam = c / visibilities["image"][j].freq / 1.0e-4
wave = lam * numpy.sqrt((1. - b) / (1. + b))
m.set_camera_wavelength(wave)
if p["docontsub"]:
m.run_image(name=visibilities["lam"][j], nphot=1e5, \
npix=visibilities["image_npix"][j], lam=None, \
pixelsize=visibilities["image_pixelsize"][j], \
tgas_eq_tdust=True, scattering_mode_max=0, \
incl_dust=True, incl_lines=True, loadlambda=True, \
incl=p["i"], pa=-p["pa"], dpc=p["dpc"], code="radmc3d",\
verbose=False, setthreads=ncpus)
m.run_image(name="cont", nphot=1e5, \
npix=visibilities["image_npix"][j], lam=None, \
pixelsize=visibilities["image_pixelsize"][j], \
tgas_eq_tdust=True, scattering_mode_max=0, \
incl_dust=True, incl_lines=False, loadlambda=True, \
incl=p["i"], pa=-p["pa"], dpc=p["dpc"], code="radmc3d",\
verbose=False, setthreads=ncpus)
m.images[visibilities["lam"]
[j]].image -= m.images["cont"].image
else:
m.run_image(name=visibilities["lam"][j], nphot=1e5, \
npix=visibilities["image_npix"][j], lam=None, \
pixelsize=visibilities["image_pixelsize"][j], \
tgas_eq_tdust=True, scattering_mode_max=0, \
incl_dust=False, incl_lines=True, loadlambda=True, \
incl=p["i"], pa=-p["pa"], dpc=p["dpc"], code="radmc3d",\
verbose=False, setthreads=ncpus)
x, y = numpy.meshgrid(numpy.linspace(-256,255,512), \
numpy.linspace(-256,255,512))
beam = misc.gaussian2d(x, y, 0., 0., \
visibilities["image"][j].header["BMAJ"]/2.355/\
visibilities["image"][j].header["CDELT2"], \
visibilities["image"][j].header["BMIN"]/2.355/\
visibilities["image"][j].header["CDELT2"], \
(90-visibilities["image"][j].header["BPA"])*\
numpy.pi/180., 1.0)
for ind in range(len(wave)):
m.images[visibilities["lam"][j]].image[:,:,ind,0] = \
scipy.signal.fftconvolve(\
m.images[visibilities["lam"][j]].image[:,:,ind,0], \
beam, mode="same")
os.system("rm params.txt")
os.chdir(original_dir)
os.system("rmdir /tmp/temp_{1:s}_{0:d}".format(comm.Get_rank(), source))
return m
lam = data[:,0].copy() * 1.0e-4
kabs = data[:,1].copy()
ksca = data[:,2].copy()
d = dust.Dust()
d.set_properties(lam, kabs, ksca)
# Read in the gas information.
g = gas.Gas()
g.set_properties_from_lambda(gas.__path__[0]+"/data/co.dat")
# Generate the model.
m = modeling.YSOModel()
m.add_star(mass=0.5, luminosity=1.0, temperature=4000.)
m.set_spherical_grid(0.1, 1000., 100, 100, 2, code="radmc3d")
m.add_pringle_disk(mass=0.0001, rmin=0.1, rmax=50., plrho=2., h0=0.1, plh=1.0, \
dust=d, t0=100, plt=0.25, gas=[g], abundance=[1.0e-4], aturb=0.1)
m.add_ulrich_envelope(mass=0.000001, rmin=0.1, rmax=1000., rcent=50, cavpl=1., \
cavrfact=1., dust=d, t0=100, tpl=0.25, gas=[g], abundance=[1.0e-4], \
aturb=0.1)
m.grid.set_wavelength_grid(0.1,1.0e5,500,log=True)
# Run the image.