def new_disk_with_bump(Mstar=1 | units.MSun,
Ndisk=100,
Mdisk=0.9 | units.MSun,
Rmin=1.0 | units.AU,
Rmax=100.0 | units.AU,
Mbump=0.1 | units.MSun,
Rbump=10.0 | units.AU,
abump=10 | units.AU):
converter = nbody_system.nbody_to_si(Mdisk, Rmin)
from amuse.ext.protodisk import ProtoPlanetaryDisk
bodies = ProtoPlanetaryDisk(Ndisk,
convert_nbody=converter,
densitypower=1.5,
Rmin=1,
Rmax=Rmax / Rmin,
q_out=1.0,
discfraction=1.0).result
Mdisk = bodies.mass.sum()
bodies.move_to_center()
com = bodies.center_of_mass()
mm = Mdisk / float(Ndisk)
Nbump = Mbump / mm
bump = new_plummer_gas_model(Nbump,
convert_nbody=nbody_system.nbody_to_si(
Mbump, Rbump))
bump.x += abump
r_bump = abump
inner_particles = bodies.select(lambda r: (com - r).length() < abump,
["position"])
M_inner = inner_particles.mass.sum() + Mstar
v_circ = (constants.G * M_inner *
(2. / r_bump - 1. / abump)).sqrt().value_in(units.kms)
bump.velocity += [0, v_circ, 0] | units.kms
bodies.add_particles(bump)
bodies = bodies.select(lambda r: (com - r).length() > Rmin, ["position"])
bodies = bodies.select(lambda r: (com - r).length() < Rmax, ["position"])
print("Nbump=", Ndisk, Mbump, Rbump, Nbump)
print("Mass =", Mstar, Mdisk,
bodies.mass.sum().in_(units.MSun),
bodies.mass.sum() / Mstar)
print("X-min/max:", min(bodies.x), max(bodies.x))
bodies = bodies.select(lambda r: r.length() < 1.0 * Rmax, ["position"])
print("X-min/max:", min(bodies.x), max(bodies.x))
return bodies
def initial_conditions(Q, N, Rmax, diskmassfrac, seed_disk):
'''
returns Sun + 8 planets, as well as a disk around Neptune
'''
#get the solar system objects
sun_and_planets = new_solar_system()
#throw out Pluto, get Neptune object from new_solar_system
N_particles = len(sun_and_planets)
sun_and_planets = sun_and_planets[:N_particles - 1]
Nep_ind = len(sun_and_planets) - 1
Sun = sun_and_planets[0]
Neptune = sun_and_planets[Nep_ind]
#hill radius of Neptune
a_Neptune = np.sqrt(Neptune.x**2 + Neptune.y**2 + Neptune.z**2)
Neptune_Hill = a_Neptune * (Neptune.mass / Sun.mass)**(1 / 3.)
#get the disk with appropriate Salpeter mass distribution
#Salpeter mass function with a range of 1 order of magnitude
mmin = 0.0005 * Neptune.mass #mmax goes to 0.005
masses = new_salpeter_mass_distribution(N,
mass_min=mmin,
mass_max=(10 * mmin))
#set up converter, protoplanetary disk gas particles
np.random.seed(seed_disk) #random seed for the disk
converter_gas = nbody_system.nbody_to_si(Neptune.mass, Rmax | units.AU)
gas = ProtoPlanetaryDisk(N,
convert_nbody=converter_gas,
Rmin=converter_gas.to_nbody(Neptune_Hill).number,
Rmax=converter_gas.to_nbody(Rmax
| units.AU).number,
q_out=Q,
discfraction=diskmassfrac).result
#attribute Salpeter masses to the gas
gas.mass = masses
#move disk to Neptune's phase space coordinates
gas.x += Neptune.x
gas.y += Neptune.y
gas.z += Neptune.z
gas.vx += Neptune.vx
gas.vy += Neptune.vy
gas.vz += Neptune.vz
return sun_and_planets, gas
def new_disk_with_bump(Mstar = 10|units.MSun,
Ndisk=100, Mdisk=1.0|units.MSun,
Rmin=1.0|units.AU, Rmax=100.0|units.AU,
Mbump=0.1|units.MSun,Rbump=5.0|units.AU,
abump=10|units.AU):
converter=nbody_system.nbody_to_si(Mstar, Rmin)
disk = ProtoPlanetaryDisk(Ndisk, convert_nbody=converter,
densitypower=1.5, Rmin=1, Rmax=Rmax/Rmin,
q_out=1.0, discfraction=Mdisk/Mstar).result
com = disk.center_of_mass()
# determine bump's local velocity
inner_particles = disk.select(lambda r: (com-r).length()
< abump,["position"])
M_inner = Mstar + inner_particles.mass.sum()
v_circ = (constants.G*M_inner*(2./abump - 1./abump)) \
.sqrt().value_in(units.kms)
# initialize bump
Nbump = int(Ndisk*Mbump/Mdisk)
bump = new_plummer_gas_model(Nbump,
convert_nbody=nbody_system.nbody_to_si(Mbump,
Rbump))
bump.x += abump
bump.velocity += [0, v_circ, 0] | units.kms
disk.add_particles(bump)
disk.move_to_center()
return disk
def make_giant_molecular_clouds(Ngmc):
N_thick_disk = int(0.5 * Ngmc)
N_thin_disk = int(0.5 * Ngmc)
converter = nbody_system.nbody_to_si(1.e+8 | units.MSun, 1.0 | units.kpc)
from amuse.ext.protodisk import ProtoPlanetaryDisk
Rin = 3.5 | units.kpc
Rout = 7.5 | units.kpc
masses = new_powerlaw_mass_distribution(N_thick_disk,
alpha=-1.6,
mass_min=1.0e+3 | units.MSun,
mass_max=1.0e+8 | units.MSun)
MGMCs = masses.sum()
MWG = MilkyWay_galaxy()
v_inner = MWG.vel_circ(Rout)
MGalaxy = v_inner**2 * Rout / constants.G
print("Masses:", MGMCs.in_(units.MSun), MGalaxy.in_(units.MSun), \
MGMCs/MGalaxy)
GMCs = ProtoPlanetaryDisk(len(masses),
convert_nbody=converter,
Rmin=Rin.value_in(units.kpc),
Rmax=Rout.value_in(units.kpc),
q_out=30.0,
discfraction=MGMCs / MGalaxy).result
#second population of GMCs
masses = new_powerlaw_mass_distribution(len(GMCs),
alpha=-1.6,
mass_min=1.e+3 | units.MSun,
mass_max=1.0e+8 | units.MSun)
GMCs.mass = masses
MGMCs = masses.sum()
thin_disk_GMCs = ProtoPlanetaryDisk(N_thin_disk,
convert_nbody=converter,
Rmin=Rin.value_in(units.kpc),
Rmax=2 * Rout.value_in(units.kpc),
q_out=10.0,
discfraction=MGMCs / MGalaxy).result
thin_disk_GMCs.masses = masses
GMCs.add_particles(thin_disk_GMCs)
GMCs.velocity *= -1
GMCs.mass = new_powerlaw_mass_distribution(len(GMCs),
alpha=-1.6,
mass_min=1.e+3 | units.MSun,
mass_max=1.0e+8 | units.MSun)
print("v=", v_inner.in_(units.kms))
print("GMC mass=", GMCs.mass.sum().in_(units.MSun))
for gi in range(len(GMCs)):
r = GMCs[gi].position.length()
vc = MWG.vel_circ(r)
GMCs[gi].velocity = GMCs[gi].velocity * (vc /
GMCs[gi].velocity.length())
return GMCs
def main(t_end, dt):
stars = init_sun_jupiter()
Sun = stars[0]
Jupiter = stars[1]
orbit0 = orbital_elements_from_binary(stars, G=constants.G)
a0 = orbit0[2].in_(units.AU)
e0 = orbit0[3]
Hill_radius0 = a0 * (1 - e0) * (
(1.0 | units.MJupiter).value_in(units.MSun) / 3.)**(1. / 3.)
eps = 1 | units.RSun
gravity = Gravity(ph4, stars, eps)
N = 500
Rmin = 1.0
Rmax = 100.0
converter = nbody_system.nbody_to_si(1.0 | units.MSun, 1.0 | units.AU)
np.random.seed(1)
disk = ProtoPlanetaryDisk(N, convert_nbody=converter, densitypower=1.5,\
Rmin=Rmin, Rmax=Rmax, q_out=1., discfraction=0.01)
gas = disk.result
gas.h_smooth = 0.06 | units.AU
hydro = Hydro(Fi, gas, eps, dt)
sink = init_sink_particle(0. | units.MSun, Hill_radius0, Jupiter.position,
Jupiter.velocity)
hydro.particles.add_particles(sink)
a_Jup, e_Jup, times = gravity_hydro_bridge(gravity, hydro, t_end, dt)
return a_Jup, e_Jup, times
def new_disk_with_bump(Mstar = 1|units.MSun,
Ndisk=100, Mdisk=0.9|units.MSun,
Rmin=1.0|units.AU, Rmax=100.0|units.AU,
Mbump=0.1|units.MSun,Rbump=10.0|units.AU,
abump=10|units.AU):
converter=nbody_system.nbody_to_si(Mdisk, Rmin)
bodies = ProtoPlanetaryDisk(Ndisk, convert_nbody=converter,
densitypower=1.5,
Rmin=1.0,
Rmax=Rmax/Rmin,
q_out=1.0,
discfraction=1.0).result
Mdisk = bodies.mass.sum()
bodies.move_to_center()
com = bodies.center_of_mass()
mm = Mdisk/float(Ndisk)
Nbump = Mbump/mm
print "Nbump=", Mbump, Rbump, Nbump
print "Mass =", Mstar, Mdisk, bodies.mass.sum().in_(units.MSun), bodies.mass.sum()/Mstar
bump = new_plummer_gas_model(Nbump, convert_nbody=nbody_system.nbody_to_si(Mbump, Rbump))
bump.x += abump
r_bump = abump
inner_particles = bodies.select(lambda r: (com-r).length()<abump,["position"])
M_inner = inner_particles.mass.sum() + Mstar
v_circ = (constants.G*M_inner*(2./r_bump - 1./abump)).sqrt().value_in(units.kms)
bump.velocity += [0, v_circ, 0] | units.kms
bodies.add_particles(bump)
return bodies
def new_disk(Mstar=1 | units.MSun,
Ndisk=500,
Rmin=1.0 | units.AU,
Rmax=100.0 | units.AU):
Mdisk = 0.01 * Mstar #setting the mass of the disk to 1% of star
# Initialise disk
converter = nbody_system.nbody_to_si(Mstar, Rmin)
disk = ProtoPlanetaryDisk(Ndisk,
convert_nbody=converter,
densitypower=1.5,
Rmin=1,
Rmax=Rmax / Rmin,
q_out=1.0,
discfraction=Mdisk / Mstar).result
com = disk.center_of_mass()
return disk
def create_disc(self):
#The following line makes sure masses for ISM and disc particles are equal:
self.discfraction = (
self.disc_N *
(self.ism_slice_mass / self.ism_slice_N)) / self.Mstar
T_disc = self.T
cs_disc = ((T_disc * constants.kB) / self.mu).sqrt()
densitypower = 1.5
g2 = 2 - densitypower
k_out = ((1 + self.discfraction) / self.disc_Rmax**3)**0.5
sigma_out = g2 * self.discfraction / (
2 * numpy.pi * self.disc_Rmax**densitypower *
(self.disc_Rmax**g2 - self.disc_Rmin**g2))
q_out = self.converter.to_generic(cs_disc).value_in(
nbody_system.length / nbody_system.time) / (numpy.pi * sigma_out /
k_out)
print "Number of disk particles:", self.disc_N
proto = ProtoPlanetaryDisk(self.disc_N,
convert_nbody=self.converter,
discfraction=self.discfraction,
densitypower=1.5,
thermalpower=0,
Rmin=self.disc_Rmin,
Rmax=self.disc_Rmax,
q_out=q_out)
disc = proto.result
print "The mass of a disc particle = ", disc.mass[0].value_in(units.kg)
#Rotate 90 degrees with respect to the z-axis and then theta degrees with respect to the y-axis
temp_x = disc[:].x
temp_y = disc[:].y
temp_z = disc[:].z
temp_vx = disc[:].vx
temp_vy = disc[:].vy
temp_vz = disc[:].vz
disc.x = temp_z * numpy.cos(self.disc_angle) - temp_y * numpy.sin(
self.disc_angle)
disc.y = temp_z * numpy.sin(self.disc_angle) + temp_y * numpy.cos(
self.disc_angle)
disc.z = -temp_x
disc.vx = temp_vz * numpy.cos(self.disc_angle) - temp_vy * numpy.sin(
self.disc_angle)
disc.vy = temp_vz * numpy.sin(self.disc_angle) + temp_vy * numpy.cos(
self.disc_angle)
disc.vz = -temp_vx
return disc
def main(N=1000, Lstar=100| units.LSun, boxsize=10| units.parsec,
rho=1.0| (units.amu/units.cm**3), t_end=0.1|units.Myr, n_steps=10):
ionization_fraction = 0.0
internal_energy = (9. |units.kms)**2
source=Particles(1)
source.position = (0, 0, 0) |units.parsec
source.flux = Lstar/(20. | units.eV)
source.luminosity = Lstar/(20. | units.eV)
source.rho = rho
source.xion = ionization_fraction
source.u = internal_energy
converter=nbody_system.nbody_to_si(1|units.MSun, boxsize)
ism = ProtoPlanetaryDisk(N, convert_nbody=converter,
densitypower=1.5,
Rmin=0.1,
Rmax=1,
q_out=1.0,
discfraction=1.0).result
ism = ism.select(lambda r: r.length()<0.5*boxsize,["position"])
gamma=5./3.
mu=1.| units.amu
Tinit = 10000|units.K
ism.u = 1/(gamma-1)*constants.kB * Tinit/mu
ism.rho = rho
ism.flux = 0. | units.s**-1
ism.xion = ionization_fraction
ism.h_smooth = 0 | units.AU
rad = SimpleXSplitSet(redirect="none")
# rad = SimpleX()
# rad = SPHRay()
rad.parameters.box_size=1.001*boxsize
rad.parameters.timestep=0.001 | units.Myr
rad.src_particles.add_particle(source)
rad.gas_particles.add_particles(ism)
channel_to_local_gas = rad.gas_particles.new_channel_to(ism)
write_set_to_file(ism, "rad.hdf5", 'hdf5')
time = 0.0 | t_end.unit
dt = t_end/float(n_steps)
while time<t_end:
time += dt
rad.evolve_model(time)
channel_to_local_gas.copy_attributes(["xion",])
write_set_to_file(ism, "rad.hdf5", 'hdf5')
print "Time=", time
print "min ionization:", rad.gas_particles.xion.min()
print "average Xion:", rad.gas_particles.xion.mean()
print "max ionization:", rad.gas_particles.xion.max()
rad.stop()
def main(t_end=1000. | units.yr, dt=10. | units.yr):
print 'Initializing...'
converter = nbody_system.nbody_to_si(1. | units.MSun, 1. | units.AU)
# Initialize the gravity system
Sun_and_Jupiter = init_sun_jupiter()
Sun = Sun_and_Jupiter[0]
Jupiter = Sun_and_Jupiter[1]
orbit0 = orbital_elements_from_binary(Sun_and_Jupiter, G=constants.G)
a0 = orbit0[2].in_(units.AU)
e0 = orbit0[3]
Hill_radius0 = a0 * (1 - e0) * (
(1.0 | units.MJupiter).value_in(units.MSun) / 3.)**(1. / 3.)
# Initialising the direct N-body integrator
gravity = ph4(converter)
gravity.particles.add_particle(Jupiter)
gravity.timestep = dt
# Setting proto-disk parameters
N = 4000
Mstar = 1. | units.MSun
Mdisk = 0.01 * Mstar
Rmin = 2.
Rmax = 100.
# Initialising the proto-planetary disk
np.random.seed(1)
disk = ProtoPlanetaryDisk(N,
convert_nbody=converter,
densitypower=1.5,
Rmin=Rmin,
Rmax=Rmax,
q_out=1.,
discfraction=Mdisk / Mstar)
disk_gas = disk.result
# Initialize the sink particle
sink = init_sink_particle(0. | units.MSun, Hill_radius0, Jupiter.position,
Jupiter.velocity)
# Initialising the SPH code
sph = Fi(converter, mode="openmp")
sph.gas_particles.add_particles(disk_gas)
sph.dm_particles.add_particle(Sun)
sph.parameters.timestep = dt
# bridge and evolve
a_Jup, e_Jup, disk_size, times, accreted_mass = gravity_hydro_bridge(
gravity, sph, sink, [Sun_and_Jupiter, disk_gas], Rmin, t_end, dt)
return a_Jup, e_Jup, disk_size, times, accreted_mass
def add_debris_disk(star,
ndisk_per_MSun,
fdisk,
masteroid,
Rmin,
Rmax,
alpha=1.5,
Q=1.0):
Ndisk = int(ndisk_per_MSun * star.mass.value_in(units.MSun))
print("Run with Ndisk = ", Ndisk)
converter = nbody_system.nbody_to_si(star.mass, Rmin)
disk = ProtoPlanetaryDisk(Ndisk,
convert_nbody=converter,
densitypower=alpha,
Rmin=Rmin / Rmin,
Rmax=Rmax / Rmin,
q_out=Q,
discfraction=fdisk).result
disk.mass = masteroid
disk.name = "asteroid"
disk.type = "debris"
disk.host = star.key
disk.position += star.position
disk.velocity += star.velocity
return disk
def main(t_end=1000. | units.yr, dt=10. | units.yr):
print 'Initializing...'
converter = nbody_system.nbody_to_si(1. | units.MSun, 1. | units.AU)
# Initialize the gravity system
Sun_and_Jupiter = init_sun_jupiter()
Sun = Sun_and_Jupiter[0]
Jupiter = Sun_and_Jupiter[1]
orbit0 = orbital_elements_from_binary(Sun_and_Jupiter, G=constants.G)
a0 = orbit0[2].in_(units.AU)
e0 = orbit0[3]
Hill_radius0 = a0 * (1 - e0) * (
(1.0 | units.MJupiter).value_in(units.MSun) / 3.)**(1. / 3.)
gravity = ph4(converter)
gravity.particles.add_particles(Sun_and_Jupiter)
gravity.timestep = dt
# initialize the hydrodynamics(SPH) system
# initialize the protoplanetary disk
N = 1000
Mstar = 1. | units.MSun
Mdisk = 0.01 * Mstar
Rmin = 2.
Rmax = 100.
np.random.seed(1)
disk = ProtoPlanetaryDisk(N,
convert_nbody=converter,
densitypower=1.5,
Rmin=Rmin,
Rmax=Rmax,
q_out=1.)
disk_gas = disk.result
disk_gas.h_smooth = 0.06 | units.AU
# initialize the sink particle
sink = init_sink_particle(0. | units.MSun, Hill_radius0, Jupiter.position,
Jupiter.velocity)
sph = Fi(converter)
sph.particles.add_particles(sink)
sph.gas_particles.add_particles(disk_gas)
sph.parameters.timestep = dt
# bridge and evolve
a_Jup, e_Jup, disk_size, times = gravity_hydro_bridge(gravity, sph, \
[Sun_and_Jupiter, disk_gas], Rmin, t_end, dt)
return a_Jup, e_Jup, disk_size, times
def make_giant_molecular_clouds(Ngmc):
N_thick_disk = int(0.5*Ngmc)
N_thin_disk = int(0.5*Ngmc)
converter=nbody_system.nbody_to_si(1.e+8|units.MSun, 1.0|units.kpc)
from amuse.ext.protodisk import ProtoPlanetaryDisk
Rin = 3.5 | units.kpc
Rout = 7.5 | units.kpc
masses = new_powerlaw_mass_distribution(N_thick_disk, alpha=-1.6,
mass_min=1.0e+3|units.MSun,
mass_max=1.0e+8|units.MSun)
MGMCs = masses.sum()
MWG = MilkyWay_galaxy()
v_inner = MWG.vel_circ(Rout)
MGalaxy = v_inner**2*Rout/constants.G
print "Masses:", MGMCs.in_(units.MSun), MGalaxy.in_(units.MSun), \
MGMCs/MGalaxy
GMCs = ProtoPlanetaryDisk(len(masses), convert_nbody=converter,
Rmin=Rin.value_in(units.kpc),
Rmax=Rout.value_in(units.kpc),
q_out=30.0, discfraction=MGMCs/MGalaxy).result
#second population of GMCs
masses = new_powerlaw_mass_distribution(len(GMCs), alpha=-1.6,
mass_min=1.e+3|units.MSun,
mass_max=1.0e+8|units.MSun)
GMCs.mass = masses
MGMCs = masses.sum()
thin_disk_GMCs = ProtoPlanetaryDisk(N_thin_disk, convert_nbody=converter,
Rmin=Rin.value_in(units.kpc),
Rmax=2*Rout.value_in(units.kpc),
q_out=10.0, discfraction=MGMCs/MGalaxy).result
thin_disk_GMCs.masses = masses
GMCs.add_particles(thin_disk_GMCs)
GMCs.velocity *= -1
GMCs.mass = new_powerlaw_mass_distribution(len(GMCs), alpha=-1.6,
mass_min=1.e+3|units.MSun,
mass_max=1.0e+8|units.MSun)
print "v=", v_inner.in_(units.kms)
print "GMC mass=", GMCs.mass.sum().in_(units.MSun)
for gi in range(len(GMCs)):
r = GMCs[gi].position.length()
vc = MWG.vel_circ(r)
GMCs[gi].velocity = GMCs[gi].velocity * (vc/GMCs[gi].velocity.length())
return GMCs
def test_rotate(phi, theta, chi):
from amuse.ext.protodisk import ProtoPlanetaryDisk
converter = nbody_system.nbody_to_si(1.0 | units.MSun, 1.0 | units.au)
disk = ProtoPlanetaryDisk(1000,
convert_nbody=converter,
Rmin=1,
Rmax=100,
q_out=1.0,
discfraction=0.01).result
disk = rotate_particle_set(disk, phi, theta, chi)
from matplotlib import pyplot
pyplot.scatter(disk.x.value_in(units.au), disk.y.value_in(units.au))
pyplot.xlabel("x-axis [au]")
pyplot.ylabel("y-axis [au]")
pyplot.show()
pyplot.scatter(disk.x.value_in(units.au), disk.z.value_in(units.au))
pyplot.xlabel("x-axis [au]")
pyplot.ylabel("z-axis [au]")
pyplot.show()
def initialize_star_and_planetary_system(Mstar, Ndisk, Mdisk, Rmin, Rmax):
converter=nbody_system.nbody_to_si(Mstar, Rmin)
disk_massfraction = Mdisk/Mstar
disk = ProtoPlanetaryDisk(Ndisk, convert_nbody=converter,
densitypower=1.5,
Rmin=Rmin.value_in(units.AU),
Rmax=Rmax.value_in(units.AU),
q_out=1.0, discfraction=disk_massfraction).result
#disk.h_smooth= Rmin/Ndisk
star = Particles(1)
star.mass = Mstar
star.radius = 1| units.RSun
star.position = (0,0,0) | units.AU
star.velocity = (0,0,0) | units.kms
planets = make_planets_oligarch.new_system(Mstar, star.radius,
Rmin, Rmax, Mdisk)
star.add_particles(planets[0].planets)
print star
return star, disk
def init_body_solar_disk_planetary(Ndisk, Mdisk, Rmin, Rmax):
print 'Initializing...'
#converter = nbody_system.nbody_to_si(1.|units.MJupiter, 1.|units.AU)
# Initialize the solar system
Sun_Jupiter = init_sun_jupiter()
Sun = Sun_Jupiter[0]
Jupiter = Sun_Jupiter[1]
orbit = orbital_elements_from_binary(Sun_Jupiter, G=constants.G)
a = orbit[2].in_(units.AU)
e = orbit[3]
hr = Hill_radius(a, e, Sun_Jupiter)
# Initialize the proto-planetary disk
np.random.seed(1)
disk_converter = nbody_system.nbody_to_si(Sun.mass, Rmin)
disk = ProtoPlanetaryDisk(Ndisk,
convert_nbody=disk_converter,
densitypower=1.5,
Rmin=1.0,
Rmax=Rmax / Rmin,
q_out=1.0,
discfraction=Mdisk / Sun.mass)
disk_gas = disk.result
# Initialize the sink particle
sink = init_sink_particle(0. | units.MSun, hr, Jupiter.position,
Jupiter.velocity)
# Initizalize the passing star
e = 1.2
Mstar = 2.0 | units.MSun
pericenter = 200.0 | units.AU
Pstar = init_passing_star(pericenter, e, Mstar)
return Sun_Jupiter, disk_gas, sink, Pstar
Rstar = 695510000 | units.m
Mdisk = 0.01 | units.MSun
Rmin = 1
Rmax = 100
overwrite = True
d_plot_dir = 'distribution_plots_4k/'
# Setting a seed
np.random.seed(1)
# Initialising disk
convert = nbody_system.nbody_to_si(Mstar, 1. | units.AU)
proto = ProtoPlanetaryDisk(N,
convert_nbody=convert,
densitypower=1.5,
Rmin=Rmin,
Rmax=Rmax,
q_out=1.,
discfraction=Mdisk / Mstar)
disk_gas = proto.result
# Initialising star
sun = Particles(1)
sun.mass = Mstar
sun.radius = 0.1 | units.AU
sun.x = 0. | units.AU
sun.y = 0. | units.AU
sun.z = 0. | units.AU
sun.vx = 0. | units.kms
sun.vy = 0. | units.kms
sun.vz = 0. | units.kms
# Locate the star at a certain position
stars[0].x, stars[0].y, stars[
0].z = 100. | units.au, 0. | units.au, 0. | units.au
# Give it a certain velocity
stars[0].vx, stars[0].vy, stars[0].vz = 20. | (units.au / units.yr), 0. | (
units.au / units.yr), 0. | (units.au / units.yr)
# Create a converter. In this way we turn n-body system units to the physical units we are interested in
converter = nbody_system.nbody_to_si(1. | units.MSun, 1. | units.au)
# Create protoplanetary disk
N_particles = 1000 # Number of SPH particles
disk = ProtoPlanetaryDisk(N_particles,
convert_nbody=converter,
densitypower=1.5,
Rmin=0.5,
Rmax=100,
q_out=1.) # Rmin and Rmax in AU
disk_particles = disk.result # Disk particles
disk_particles.h_smooth = 0.06 | units.au # Smoothing length
# Rotate the disk 90 degrees around x axis
disk = rotate(disk_particles, 90, 0, 0)
# Start SPH code and add particles
sph = Fi(converter)
sph.gas_particles.add_particles(
disk_particles) # Disk particles are added as gas particles
sph.dm_particles.add_particles(
stars[0]) # Star is added as dark matter particle
def get_planetesimals_disk(n_disk,
r_in=20.0 | units.AU,
r_out=50.0 | units.AU,
m_star=1.0 | units.MSun,
alpha=None,
m_disk=1.0e-15 | units.MSun,
seed=42,
disk_num=1):
"""
returns particles of planetesimal disk with given parameters
"""
numpy.random.seed(seed) # Mess with random seed
for i in xrange(int(disk_num) + 4):
planetesimals = Particles(n_disk)
print "Seed:", seed
print planetesimals.key[:10]
planetesimals.mass = 0.0 | units.MJupiter
planetesimals.radius = 100.0 | units.km
planetesimals.collection_attributes.timestamp = 0.0 | units.yr
if alpha is not None:
converter = nbody_system.nbody_to_si(m_disk, r_in)
power_disk = ProtoPlanetaryDisk(n_disk,
convert_nbody=converter,
densitypower=alpha,
Rmin=1.0,
Rmax=1.0 * r_out / r_in,
q_out=0.0,
discfraction=1.0).result
x = power_disk.x
y = power_disk.y
z = power_disk.z # <--- Mystery error?
print "X"
print x.value_in(units.AU)
print "Y"
print y.value_in(units.AU)
print "Z"
print z.value_in(units.AU)
#z = 0
print "MASS"
print power_disk.mass
#power_disk.mass = 0.0 * power_disk.mass ###### THIS WORKS!!!! (if you want to switch to this later)
print power_disk.mass
a = (x**2 + y**2)**0.5
print "SM-AXIS"
print a.value_in(units.AU)
phi = numpy.arctan2(y.value_in(units.AU), x.value_in(units.AU))
vc = (constants.G * m_star / a)**0.5
vx = -vc * numpy.sin(phi)
vy = vc * numpy.cos(phi)
vz = 0.0 * vc
# vz = - vc * numpy.sin(phi) # ???????????????????????????????????????????????????????????????? #
print "VX"
print vx.value_in(units.km / units.s)
print "VY"
print vy.value_in(units.km / units.s)
print "VZ"
print vz.value_in(units.km / units.s)
print "PLANAR VELOCITY VECTOR"
print((vx**2 + vy**2)**(0.5)).value_in(units.km / units.s)
#vx = power_disk.vx
#vy = power_disk.vy
#vz = power_disk.vz
#print "POWER DISK VX"
#print vx.value_in(units.km / units.s)
#print "POWER DISK VY"
#print vy.value_in(units.km / units.s)
#print "POWER DISK VZ"
#print vz.value_in(units.km / units.s)
else:
a = r_in + (r_out - r_in) * numpy.random.rand(n_disk)
phi_rand = 2.0 * numpy.pi * numpy.random.rand(n_disk)
x = a * numpy.cos(phi_rand)
y = a * numpy.sin(phi_rand)
z = 0.0 * a
vc = (constants.G * m_star / a)**0.5
vx = -vc * numpy.sin(phi_rand)
vy = vc * numpy.cos(phi_rand)
vz = 0.0 * vc
planetesimals.x = x
planetesimals.y = y
planetesimals.z = z
planetesimals.vx = vx
planetesimals.vy = vy
planetesimals.vz = vz
return planetesimals
Sun_Jupiter = init_sun_jupiter()
Sun = Sun_Jupiter[0]
Jupiter = Sun_Jupiter[1]
orbit = orbital_elements_from_binary(Sun_Jupiter, G=constants.G)
a = orbit[2].in_(units.AU)
e = orbit[3]
hr = Hill_radius(a, e, Sun_Jupiter)
# Initialize the proto-planetary disk
np.random.seed(1)
disk_converter = nbody_system.nbody_to_si(Sun.mass, Rmin)
disk = ProtoPlanetaryDisk(Ndisk,
convert_nbody=disk_converter,
densitypower=1.5,
Rmin=1.0,
Rmax=Rmax / Rmin,
q_out=1.0,
discfraction=Mdisk / Sun.mass)
disk_gas = disk.result
# Initialize the sink particle
sink = init_sink_particle(0. | units.MSun, hr, Jupiter.position,
Jupiter.velocity)
# Initizalize the passing star
Pstar = init_passing_star(pericenter, e, Mstar)
# ------ Running the building and running hydro-code ------
# Main function
t, a_Jup, e_Jup, disk_size, accreted_mass = evolve(Sun_Jupiter, disk_gas,
def main(Ndisk, Mstar, Mdisk, Rin, Rout, t_end, Nray, x, y, z):
time = 0 | units.Myr
supernova_IIp = Supernova_IIp(10|units.day)
efficiency_factor = 0.1
Rsn = efficiency_factor * (x**2 + y**2 + z**2)**0.5
supernova = Particle()
supernova.position = (x.value_in(units.parsec),
y.value_in(units.parsec),
z.value_in(units.parsec)) |units.parsec
supernova.position *= efficiency_factor
supernova_IIp.particles.add_particle(supernova)
supernova_IIp.evolve_model(time)
supernova.luminosity = efficiency_factor**2 * supernova.luminosity
supernova.xion = 0.0
supernova.u = (10**51 | units.erg)/(10|units.MSun)
stellar = SeBa()
star = Particle()
star.mass = Mstar
star.position = (0,0,0) | units.AU
star.velocity = (0,0,0) | units.kms
stellar.particles.add_particle(star)
stellar.evolve_model(1|units.Myr)
star.luminosity = stellar.particles[0].luminosity/(20. | units.eV)
star.temperature = stellar.particles[0].temperature
stellar.stop()
star.u = (9. |units.kms)**2
star.xion = 0.0
print star
print "M=", Mdisk/Mstar
converter=nbody_system.nbody_to_si(Mstar, 1 | units.AU)
disk = ProtoPlanetaryDisk(Ndisk, convert_nbody=converter,
Rmin=Rin.value_in(units.AU),
Rmax=Rout.value_in(units.AU),
q_out=25.0, discfraction=Mdisk/Mstar).result
#### q_out=2.0, discfraction=Mdisk/Mstar).result
print disk.x.max().in_(units.AU)
print disk.mass.sum().in_(units.MSun)
print disk.u.max().in_(units.kms**2)
print disk.mass.min().in_(units.MSun)
disk.flux = 0. | units.s**-1
disk.xion = 0.0
dt = t_end/1000.
hydro = Fi(converter)
hydro.parameters.use_hydro_flag=True
hydro.parameters.radiation_flag=False
hydro.parameters.self_gravity_flag=True
hydro.parameters.gamma=1.
hydro.parameters.isothermal_flag=True
# Non-isothermal: lowest temperature remains constat at 20K
# hydro.parameters.gamma=1.66667
# hydro.parameters.isothermal_flag=False
hydro.parameters.integrate_entropy_flag=False
hydro.parameters.timestep=0.5 | units.hour #0.125 | units.day
# hydro.parameters.verbosity=99
hydro.parameters.epsilon_squared=0.1 | units.AU**2
hydro.parameters.courant=0.2
hydro.parameters.artificial_viscosity_alpha = 0.1
hydro.gas_particles.add_particles(disk)
hydro.dm_particles.add_particle(star)
hydro_to_disk = hydro.gas_particles.new_channel_to(disk)
hydro_to_star = hydro.dm_particles.new_channel_to(star.as_set())
disk_to_hydro = disk.new_channel_to(hydro.gas_particles)
star_to_hydro = star.as_set().new_channel_to(hydro.dm_particles)
hydro.evolve_model(1|units.hour)
hydro_to_disk.copy()
hydro_to_star.copy()
radiative = SPHRay(redirection="file",
number_of_workers=4)#, debugger="gdb")
radiative.parameters.number_of_rays=Nray/dt
print dt.in_(units.yr)
radiative.parameters.default_spectral_type=-3.
radiative.parameters.box_size=10000. | units.AU
radiative.parameters.ionization_temperature_solver=2
print radiative.parameters
# radiative.src_particles.add_particle(star)
radiative.src_particles.add_particle(supernova)
radiative.gas_particles.add_particles(disk)
gas_to_rad = disk.new_channel_to(radiative.gas_particles)
rad_to_gas = radiative.gas_particles.new_channel_to(disk)
print "Before"
print "Luminosity:", radiative.src_particles.luminosity
print "min ionization:", radiative.gas_particles.xion.min()
print "average Xion:", radiative.gas_particles.xion.mean()
print "max ionization:", radiative.gas_particles.xion.max()
print "min u:", radiative.gas_particles.u.min()
print "average u:", radiative.gas_particles.u.mean()
print "max u:", radiative.gas_particles.u.max()
Tmean = [] | units.K
Tmin = [] | units.K
Tmax = [] | units.K
t = [] | units.day
while radiative.model_time<t_end:
supernova = update_source_particle(radiative, time+0.5*dt, supernova,
efficiency_factor, supernova_IIp)
radiative.evolve_model(time+0.5*dt)
print "RT done at time:", time.in_(units.day)
rad_to_gas.copy()
disk_to_hydro.copy()
star_to_hydro.copy()
hydro.evolve_model(time + dt)
hydro_to_disk.copy()
hydro_to_star.copy()
supernova = update_source_particle(radiative, time+dt, supernova,
efficiency_factor, supernova_IIp)
radiative.evolve_model(time+dt)
print "RT done at time:", time.in_(units.day)
rad_to_gas.copy()
time += dt
print_diagnostics(time, supernova, disk)
Temperature = mu() / constants.kB * disk.u
t.append(time)
Tmean.append(Temperature.mean())
Tmin.append(Temperature.min())
Tmax.append(Temperature.max())
#write_set_to_file(disk, "disk_irradiation.amuse", "amuse")
print "timescale:", (disk.mass.sum().value_in(units.amu) \
/ ((Rout/Rsn)**2*supernova.luminosity)).in_(units.yr)
print "scaleheight:", abs(disk.z.value_in(units.AU)).mean()
#pyplot.hist2d(abs(disk.x.value_in(units.AU)), abs(numpy.log10(Temperature.value_in(units.K))), bins=200)
# pyplot.hist2d(abs(disk.x.value_in(units.AU)), abs(disk.z.value_in(units.AU)), bins=200)
#,norm=LogNorm())
#, Temperature.in_(units.K))
# pyplot.tripcolor(abs(disk.x.value_in(units.AU)), abs(disk.y.value_in(units.AU)), Temperature.in_(units.K))
#pyplot.hist(abs(disk.x.value_in(units.AU)), 100)
# pyplot.show()
print_diagnostics(time, supernova, disk)
#plot_ionization_fraction(disk.position, disk.xion)
# plot_ionization_fraction(disk.z, disk.u.value_in(units.kms**2))
# plot_ionization_fraction(disk.x, disk.u.value_in(units.kms**2))
radiative.stop()
plot_temperature(t, Tmin, Tmean, Tmax)
def main(t_end=1000. | units.yr, dt=10. | units.yr):
print 'Initializing...'
#converter = nbody_system.nbody_to_si(1.|units.MSun, 1.|units.AU)
# Initialize the Sun and Jupiter system
Sun, Jupiter = init_star_planet()
Sun_and_Jupiter0 = Particles()
Sun_and_Jupiter0.add_particle(Sun)
Sun_and_Jupiter0.add_particle(Jupiter)
orbit0 = orbital_elements_from_binary(Sun_and_Jupiter0, G=constants.G)
a0 = orbit0[2].in_(units.AU)
e0 = orbit0[3]
Hill_radius0 = a0 * (1 - e0) * (
(1.0 | units.MJupiter).value_in(units.MSun) / 3.)**(1. / 3.)
# Initialize the passing star
PassStar = Particle()
PassStar.mass = 2.0 | units.MSun
r_ps = 200. | units.AU
a_ps = 1000. | units.AU
mu = PassStar.mass * Sun.mass / (PassStar.mass + Sun.mass)
vx = np.sqrt(constants.G * mu * (2. / r_ps - 1. / a_ps)).in_(units.kms)
PassStar.velocity = (-vx, 0. | units.kms, 0. | units.kms)
ds = (Jupiter.position - Sun.position).value_in(units.AU)
sin_theta = ds[2] / np.sqrt(ds[0]**2 + ds[1]**2)
cos_theta = np.sqrt(1 - sin_theta**2)
PassStar.position = (Sun.position).in_(units.AU) + (
(0., 200. * cos_theta, 200. * sin_theta) | units.AU)
# Initialize the direct N-body integrator
gravity_particles = Particles()
gravity_particles.add_particle(Jupiter)
gravity_particles.add_particle(PassStar)
converter_gravity = nbody_system.nbody_to_si(
gravity_particles.mass.sum(), gravity_particles.position.length())
gravity = ph4(converter_gravity)
gravity.particles.add_particles(gravity_particles)
gravity.timestep = dt
# Set proto-disk parameters
N = 4000
Mstar = 1. | units.MSun
Mdisk = 0.01 * Mstar
Rmin = 1. | units.AU
Rmax = 100. | units.AU
# Initialize the proto-planetary disk
np.random.seed(1)
converter_disk = nbody_system.nbody_to_si(Mstar, Rmin)
disk = ProtoPlanetaryDisk(N,
convert_nbody=converter_disk,
densitypower=1.5,
Rmin=1.,
Rmax=Rmax / Rmin,
q_out=1.,
discfraction=Mdisk / Mstar)
disk_gas = disk.result
disk_star = Particles()
disk_star.add_particle(Sun)
# Initialize the sink particle
sink = init_sink_particle(0. | units.MSun, Hill_radius0, Jupiter.position,
Jupiter.velocity)
# Initialising the SPH code
#converter_hydro = nbody_system.nbody_to_si(Mdisk, Rmax)
sph = Fi(converter_disk, mode="openmp")
sph.gas_particles.add_particles(disk_gas)
sph.dm_particles.add_particle(disk_star)
sph.parameters.timestep = dt
# bridge and evolve
times, a_Jup, e_Jup, disk_size, accreted_mass = gravity_hydro_bridge(gravity, sph, sink,\
[gravity_particles, disk_star, disk_gas], Rmin, t_end, dt)
return times, a_Jup, e_Jup, disk_size, accreted_mass
def main(N=1000,
Lstar=100 | units.LSun,
boxsize=10 | units.parsec,
rho=1.0 | (units.amu / units.cm**3),
t_end=0.1 | units.Myr,
n_steps=10):
ionization_fraction = 0.0
internal_energy = (9. | units.kms)**2
source = Particles(1)
source.position = (0, 0, 0) | units.parsec
source.flux = Lstar / (20. | units.eV)
source.luminosity = Lstar / (20. | units.eV)
source.rho = rho
source.xion = ionization_fraction
source.u = internal_energy
converter = nbody_system.nbody_to_si(1 | units.MSun, boxsize)
ism = ProtoPlanetaryDisk(N,
convert_nbody=converter,
densitypower=1.5,
Rmin=0.1,
Rmax=1,
q_out=1.0,
discfraction=1.0).result
ism = ism.select(lambda r: r.length() < 0.5 * boxsize, ["position"])
gamma = 5. / 3.
mu = 1. | units.amu
Tinit = 10000 | units.K
ism.u = 1 / (gamma - 1) * constants.kB * Tinit / mu
ism.rho = rho
ism.flux = 0. | units.s**-1
ism.xion = ionization_fraction
ism.h_smooth = 0 | units.AU
rad = SimpleXSplitSet(redirect="none")
# rad = SimpleX()
# rad = SPHRay()
rad.parameters.box_size = 1.001 * boxsize
rad.parameters.timestep = 0.001 | units.Myr
rad.src_particles.add_particle(source)
rad.gas_particles.add_particles(ism)
channel_to_local_gas = rad.gas_particles.new_channel_to(ism)
write_set_to_file(ism, "rad.hdf5", 'hdf5')
time = 0.0 | t_end.unit
dt = t_end / float(n_steps)
while time < t_end:
time += dt
rad.evolve_model(time)
channel_to_local_gas.copy_attributes([
"xion",
])
write_set_to_file(ism, "rad.hdf5", 'hdf5')
print("Time=", time)
print("min ionization:", rad.gas_particles.xion.min())
print("average Xion:", rad.gas_particles.xion.mean())
print("max ionization:", rad.gas_particles.xion.max())
rad.stop()
def main(Mstar=1 | units.MSun,
Ndisk=100,
Mdisk=0.9 | units.MSun,
Rmin=1.0 | units.AU,
Rmax=100.0 | units.AU,
Mbump=0.1 | units.MSun,
Rbump=10.0 | units.AU,
abump=10 | units.AU,
t_end=1,
n_steps=10):
converter = nbody_system.nbody_to_si(Mdisk, Rmin)
from amuse.ext.protodisk import ProtoPlanetaryDisk
bodies = ProtoPlanetaryDisk(Ndisk,
convert_nbody=converter,
densitypower=1.5,
Rmin=1.0,
Rmax=Rmax / Rmin,
q_out=1.0,
discfraction=1.0).result
Mdisk = bodies.mass.sum()
bodies.move_to_center()
com = bodies.center_of_mass()
mm = Mdisk / float(Ndisk)
Nbump = int(Mbump / mm)
bump = new_plummer_gas_model(Nbump,
convert_nbody=nbody_system.nbody_to_si(
Mbump, Rbump))
bump.x += abump
r_bump = abump
inner_particles = bodies.select(lambda r: (com - r).length() < abump,
["position"])
M_inner = inner_particles.mass.sum() + Mstar
v_circ = (constants.G * M_inner *
(2. / r_bump - 1. / abump)).sqrt().value_in(units.kms)
bump.velocity += [0, v_circ, 0] | units.kms
bodies.add_particles(bump)
star = Particles(1)
star.mass = Mstar
star.radius = Rmin
star.position = [0, 0, 0] | units.AU
star.velocity = [0, 0, 0] | units.kms
import math
P_bump = (abump**3 * 4 * math.pi**2 / (constants.G *
(Mbump + Mstar))).sqrt()
t_end *= P_bump
hydro = Gadget2(converter)
hydro.gas_particles.add_particles(bodies)
hydro.dm_particles.add_particles(star)
Etot_init = hydro.kinetic_energy + hydro.potential_energy + hydro.thermal_energy
particles = ParticlesSuperset([star, bodies])
particles.move_to_center()
particles.new_channel_to(hydro.particles).copy()
bodies.h_smooth = Rmin # for the plotting routine
channel_to_star = hydro.dm_particles.new_channel_to(star)
channel_to_bodies = hydro.gas_particles.new_channel_to(bodies)
write_set_to_file(star, "stars.hdf5", "hdf5")
write_set_to_file(bodies, "hydro.hdf5", "hdf5")
time = 0.0 | t_end.unit
dt = t_end / float(n_steps)
while time < t_end:
time += dt
hydro.evolve_model(time)
channel_to_star.copy()
channel_to_bodies.copy()
write_set_to_file(star, "stars.hdf5", "hdf5")
write_set_to_file(bodies, "hydro.hdf5", "hdf5")
star.radius = Rmin
from hydro_sink_particles import hydro_sink_particles
lost = hydro_sink_particles(star, bodies)
if len(lost) > 0:
hydro.particles.remove_particles(lost)
hydro.particles.synchronize_to(particles)
print("Disk=", hydro.model_time, len(bodies), len(lost),
lost.mass.sum(), star.mass)
Ekin = hydro.kinetic_energy
Epot = hydro.potential_energy
Eth = hydro.thermal_energy
Etot = Ekin + Epot + Eth
print("T=",
hydro.get_time(),
"M=",
hydro.gas_particles.mass.sum(),
end=' ')
print("E= ", Etot, "Q= ", (Ekin + Eth) / Epot, "dE=",
(Etot_init - Etot) / Etot)
print("Star=", hydro.model_time, star[0].mass, star[0].position)
hydro.stop()
def main(Mstar=1, Ndisk=100, Mdisk= 0.001, Rmin=1, Rmax=100, t_end=10, n_steps=10, filename="nbody.hdf5"):
# numpy.random.seed(111)
Mstar = Mstar | units.MSun
Mdisk = Mdisk | units.MSun
Rmin = Rmin | units.AU
Rmax = Rmax | units.AU
t_end = t_end | units.yr
# converter=nbody_system.nbody_to_si(Mdisk, Rmax)
converter=nbody_system.nbody_to_si(Mstar, Rmin)
disk = ProtoPlanetaryDisk(Ndisk, convert_nbody=converter, densitypower=1.5,
Rmin=Rmin.value_in(units.AU),
Rmax=Rmax.value_in(units.AU),q_out=1.0,
discfraction=1.0).result
disk.move_to_center()
center_of_mass = disk.center_of_mass()
print center_of_mass
a_bump = 50
Rbump = 10 | units.AU
bump_location = center_of_mass + ([0, a_bump, 0] | units.AU)
bump_particles = disk.select(lambda r: (center_of_mass-r).length()<Rbump,["position"])
Mbump =bump_particles.mass.sum()
Nbump = len(bump_particles)
print "Nbump=", len(bump_particles), Mbump, Rbump, Nbump
print "Mass =", Mstar, Mdisk, disk.mass.sum().in_(units.MSun), disk.mass.sum()/Mstar
bump = new_plummer_gas_model(Nbump, convert_nbody=nbody_system.nbody_to_si(0.1*Mbump, Rbump))
a_bump = a_bump | units.AU
bump.x += a_bump
r_bump = a_bump
inner_particles = disk.select(lambda r: (center_of_mass-r).length()<a_bump,["position"])
M_inner = inner_particles.mass.sum() + Mstar
v_circ = (constants.G*M_inner*(2./r_bump - 1./a_bump)).sqrt().value_in(units.kms)
bump.velocity += [0, v_circ, 0] | units.kms
print "MM=", M_inner, v_circ
disk.add_particles(bump)
disk.h_smooth= Rmin/(Ndisk+Nbump)
star=Particles(1)
star.mass=Mstar
star.radius=1. | units.RSun
star.position = [0, 0, 0] | units.AU
star.velocity = [0, 0, 0] | units.kms
# star2=Particles(1)
# star2.mass=Mstar
# star2.radius=1. | units.RSun
# star2.position = [1, 0, 0] | units.AU
# star2.velocity = [0, 30, 0] | units.kms
hydro=Fi(converter)
# hydror = Fi(channel_type="ibis", hostname="galgewater")
hydro.parameters.use_hydro_flag=True
hydro.parameters.radiation_flag=False
hydro.parameters.self_gravity_flag=True
hydro.parameters.gamma=1.
hydro.parameters.isothermal_flag=True
hydro.parameters.integrate_entropy_flag=False
hydro.parameters.timestep=0.125 | units.yr
hydro.gas_particles.add_particles(disk)
gravity = Hermite(converter)
gravity.particles.add_particles(star)
# gravity.particles.add_particles(star2)
# gravity.particles.move_to_center()
channel_from_gravity_to_framework = gravity.particles.new_channel_to(star)
channel_from_hydro_to_framework = hydro.particles.new_channel_to(disk)
# make a repository of the star+disk particles in moving bodies
# moving_bodies = star.union(disk)
moving_bodies = ParticlesSuperset([star, disk])
moving_bodies.move_to_center()
write_set_to_file(moving_bodies, filename, 'hdf5')
gravity_hydro = bridge.Bridge(use_threading=False)
gravity_hydro.add_system(gravity, (hydro,) )
gravity_hydro.add_system(hydro, (gravity,) )
Etot_init = gravity_hydro.kinetic_energy + gravity_hydro.potential_energy
Etot_prev = Etot_init
time = 0.0 | t_end.unit
dt = t_end/float(n_steps)
gravity_hydro.timestep = dt/10.
while time < t_end:
time += dt
gravity_hydro.evolve_model(time)
Etot_prev_se = gravity_hydro.kinetic_energy + gravity_hydro.potential_energy
channel_from_gravity_to_framework.copy()
channel_from_hydro_to_framework.copy()
write_set_to_file(moving_bodies, filename, 'hdf5')
Ekin = gravity_hydro.kinetic_energy
Epot = gravity_hydro.potential_energy
Etot = Ekin + Epot
print "T=", time,
print "E= ", Etot, "Q= ", Ekin/Epot,
print "dE=", (Etot_init-Etot)/Etot, "ddE=", (Etot_prev-Etot)/Etot
print "star=", star
Etot_prev = Etot
gravity_hydro.stop()
def main(Mstar=1,
Ndisk=100,
Mdisk=0.001,
Rmin=1,
Rmax=100,
t_end=10,
n_steps=10,
filename="nbody.hdf5"):
# numpy.random.seed(111)
Mstar = Mstar | units.MSun
Mdisk = Mdisk | units.MSun
Rmin = Rmin | units.AU
Rmax = Rmax | units.AU
t_end = t_end | units.yr
# converter=nbody_system.nbody_to_si(Mdisk, Rmax)
converter = nbody_system.nbody_to_si(Mstar, Rmin)
disk = ProtoPlanetaryDisk(Ndisk,
convert_nbody=converter,
densitypower=1.5,
Rmin=Rmin.value_in(units.AU),
Rmax=Rmax.value_in(units.AU),
q_out=1.0,
discfraction=1.0).result
disk.move_to_center()
center_of_mass = disk.center_of_mass()
print(center_of_mass)
a_bump = 50
Rbump = 10 | units.AU
bump_location = center_of_mass + ([0, a_bump, 0] | units.AU)
bump_particles = disk.select(
lambda r: (center_of_mass - r).length() < Rbump, ["position"])
Mbump = bump_particles.mass.sum()
Nbump = len(bump_particles)
print("Nbump=", len(bump_particles), Mbump, Rbump, Nbump)
print("Mass =", Mstar, Mdisk,
disk.mass.sum().in_(units.MSun),
disk.mass.sum() / Mstar)
bump = new_plummer_gas_model(Nbump,
convert_nbody=nbody_system.nbody_to_si(
0.1 * Mbump, Rbump))
a_bump = a_bump | units.AU
bump.x += a_bump
r_bump = a_bump
inner_particles = disk.select(
lambda r: (center_of_mass - r).length() < a_bump, ["position"])
M_inner = inner_particles.mass.sum() + Mstar
v_circ = (constants.G * M_inner *
(2. / r_bump - 1. / a_bump)).sqrt().value_in(units.kms)
bump.velocity += [0, v_circ, 0] | units.kms
print("MM=", M_inner, v_circ)
disk.add_particles(bump)
disk.h_smooth = Rmin / (Ndisk + Nbump)
star = Particles(1)
star.mass = Mstar
star.radius = 1. | units.RSun
star.position = [0, 0, 0] | units.AU
star.velocity = [0, 0, 0] | units.kms
# star2=Particles(1)
# star2.mass=Mstar
# star2.radius=1. | units.RSun
# star2.position = [1, 0, 0] | units.AU
# star2.velocity = [0, 30, 0] | units.kms
hydro = Fi(converter)
# hydror = Fi(channel_type="ibis", hostname="galgewater")
hydro.parameters.use_hydro_flag = True
hydro.parameters.radiation_flag = False
hydro.parameters.self_gravity_flag = True
hydro.parameters.gamma = 1.
hydro.parameters.isothermal_flag = True
hydro.parameters.integrate_entropy_flag = False
hydro.parameters.timestep = 0.125 | units.yr
hydro.gas_particles.add_particles(disk)
gravity = Hermite(converter)
gravity.particles.add_particles(star)
# gravity.particles.add_particles(star2)
# gravity.particles.move_to_center()
channel_from_gravity_to_framework = gravity.particles.new_channel_to(star)
channel_from_hydro_to_framework = hydro.particles.new_channel_to(disk)
# make a repository of the star+disk particles in moving bodies
# moving_bodies = star.union(disk)
moving_bodies = ParticlesSuperset([star, disk])
moving_bodies.move_to_center()
write_set_to_file(moving_bodies, filename, 'hdf5')
gravity_hydro = bridge.Bridge(use_threading=False)
gravity_hydro.add_system(gravity, (hydro, ))
gravity_hydro.add_system(hydro, (gravity, ))
Etot_init = gravity_hydro.kinetic_energy + gravity_hydro.potential_energy
Etot_prev = Etot_init
time = 0.0 | t_end.unit
dt = t_end / float(n_steps)
gravity_hydro.timestep = dt / 10.
while time < t_end:
time += dt
gravity_hydro.evolve_model(time)
Etot_prev_se = gravity_hydro.kinetic_energy + gravity_hydro.potential_energy
channel_from_gravity_to_framework.copy()
channel_from_hydro_to_framework.copy()
write_set_to_file(moving_bodies, filename, 'hdf5')
Ekin = gravity_hydro.kinetic_energy
Epot = gravity_hydro.potential_energy
Etot = Ekin + Epot
print("T=", time, end=' ')
print("E= ", Etot, "Q= ", Ekin / Epot, end=' ')
print("dE=", (Etot_init - Etot) / Etot, "ddE=",
(Etot_prev - Etot) / Etot)
print("star=", star)
Etot_prev = Etot
gravity_hydro.stop()
def main(Ndisk, Mstar, Mdisk, Rin, Rout, t_end, Nray, x, y, z):
time = 0 | units.Myr
supernova_IIp = Supernova_IIp(10|units.day)
efficiency_factor = 0.1
Rsn = efficiency_factor * (x**2 + y**2 + z**2)**0.5
supernova=Particle()
supernova.position = (x.value_in(units.parsec),
y.value_in(units.parsec),
z.value_in(units.parsec)) |units.parsec
supernova.position *= efficiency_factor
supernova.luminosity = efficiency_factor**2 * supernova_IIp.luminosity_at_time(time)/(20.|units.eV)
# supernova.flux = supernova.luminosity
supernova.xion = 0.0
supernova.u = (10**51 | units.erg)/(10|units.MSun)
stellar = SeBa()
star = Particle()
star.mass = Mstar
star.position = (0,0,0) | units.AU
star.velocity = (0,0,0) | units.kms
stellar.particles.add_particle(star)
stellar.evolve_model(1|units.Myr)
star.luminosity = stellar.particles[0].luminosity/(20. | units.eV)
star.temperature = stellar.particles[0].temperature
stellar.stop()
star.u = (9. |units.kms)**2
star.xion = 0.0
print star
print "M=", Mdisk/Mstar
converter=nbody_system.nbody_to_si(Mstar, 1 | units.AU)
disk = ProtoPlanetaryDisk(Ndisk, convert_nbody=converter,
Rmin=Rin.value_in(units.AU),
Rmax=Rout.value_in(units.AU),
q_out=25.0, discfraction=Mdisk/Mstar).result
#### q_out=2.0, discfraction=Mdisk/Mstar).result
print disk.x.max().in_(units.AU)
print disk.mass.sum().in_(units.MSun)
print disk.u.max().in_(units.kms**2)
print disk.mass.min().in_(units.MSun)
disk.flux = 0. | units.s**-1
disk.xion = 0.0
dt = t_end/1000.
hydro = Fi(converter)
hydro.parameters.use_hydro_flag=True
hydro.parameters.radiation_flag=False
hydro.parameters.self_gravity_flag=True
hydro.parameters.gamma=1.
hydro.parameters.isothermal_flag=True
# Non-isothermal: lowest temperature remains constat at 20K
# hydro.parameters.gamma=1.66667
# hydro.parameters.isothermal_flag=False
hydro.parameters.integrate_entropy_flag=False
hydro.parameters.timestep=0.5 | units.hour #0.125 | units.day
# hydro.parameters.verbosity=99
hydro.parameters.epsilon_squared=0.1 | units.AU**2
hydro.parameters.courant=0.2
hydro.parameters.artificial_viscosity_alpha = 0.1
hydro.gas_particles.add_particles(disk)
hydro.dm_particles.add_particle(star)
hydro_to_disk = hydro.gas_particles.new_channel_to(disk)
hydro_to_star = hydro.dm_particles.new_channel_to(star.as_set())
disk_to_hydro = disk.new_channel_to(hydro.gas_particles)
star_to_hydro = star.as_set().new_channel_to(hydro.dm_particles)
hydro.evolve_model(1|units.hour)
hydro_to_disk.copy()
hydro_to_star.copy()
radiative = SPHRay(redirection="file", number_of_workers=4)#, debugger="gdb")
radiative.parameters.number_of_rays=Nray/dt
print dt.in_(units.yr)
radiative.parameters.default_spectral_type=-3.
radiative.parameters.box_size=10000. | units.AU
radiative.parameters.ionization_temperature_solver=2
print radiative.parameters
# radiative.src_particles.add_particle(star)
radiative.src_particles.add_particle(supernova)
radiative.gas_particles.add_particles(disk)
gas_to_rad = disk.new_channel_to(radiative.gas_particles)
rad_to_gas = radiative.gas_particles.new_channel_to(disk)
print "Before"
print "Luminosity:", radiative.src_particles.luminosity
print "min ionization:", radiative.gas_particles.xion.min()
print "average Xion:", radiative.gas_particles.xion.mean()
print "max ionization:", radiative.gas_particles.xion.max()
print "min u:", radiative.gas_particles.u.min()
print "average u:", radiative.gas_particles.u.mean()
print "max u:", radiative.gas_particles.u.max()
Tmean = [] | units.K
Tmin = [] | units.K
Tmax = [] | units.K
t = [] | units.day
while radiative.model_time<t_end:
supernova = update_source_particle(radiative, time+0.5*dt, supernova, efficiency_factor, supernova_IIp)
radiative.evolve_model(time+0.5*dt)
print "RT done at time:", time.in_(units.day)
rad_to_gas.copy()
disk_to_hydro.copy()
star_to_hydro.copy()
hydro.evolve_model(time + dt)
hydro_to_disk.copy()
hydro_to_star.copy()
supernova = update_source_particle(radiative, time+dt, supernova, efficiency_factor, supernova_IIp)
radiative.evolve_model(time+dt)
print "RT done at time:", time.in_(units.day)
rad_to_gas.copy()
time += dt
print_diagnostics(time, supernova, disk)
Temperature = mu() / constants.kB * disk.u
t.append(time)
Tmean.append(Temperature.mean())
Tmin.append(Temperature.min())
Tmax.append(Temperature.max())
#write_set_to_file(disk, "disk_irradiation.amuse", "amuse")
print "timescale:", (disk.mass.sum().value_in(units.amu)/((Rout/Rsn)**2*supernova.luminosity)).in_(units.yr)
print "scaleheight:", abs(disk.z.value_in(units.AU)).mean()
#pyplot.hist2d(abs(disk.x.value_in(units.AU)), abs(numpy.log10(Temperature.value_in(units.K))), bins=200)
# pyplot.hist2d(abs(disk.x.value_in(units.AU)), abs(disk.z.value_in(units.AU)), bins=200)
#,norm=LogNorm())
#, Temperature.in_(units.K))
# pyplot.tripcolor(abs(disk.x.value_in(units.AU)), abs(disk.y.value_in(units.AU)), Temperature.in_(units.K))
#pyplot.hist(abs(disk.x.value_in(units.AU)), 100)
# pyplot.show()
print_diagnostics(time, supernova, disk)
#plot_ionization_fraction(disk.position, disk.xion)
# plot_ionization_fraction(disk.z, disk.u.value_in(units.kms**2))
# plot_ionization_fraction(disk.x, disk.u.value_in(units.kms**2))
radiative.stop()
plot_temperature(t, Tmin, Tmean, Tmax)
x, y, z, vx, vy, vz)
rho = rho.reshape((N + 1, N + 1))
return numpy.transpose(rho)
if __name__ == "__main__":
N = 20000
tend = 10. | units.yr
Mstar = 1. | units.MSun
convert = nbody_system.nbody_to_si(Mstar, 1. | units.AU)
proto = ProtoPlanetaryDisk(N,
convert_nbody=convert,
densitypower=1.5,
Rmin=4,
Rmax=20,
q_out=1.)
gas = proto.result
gas.h_smooth = 0.06 | units.AU
sun = Particles(1)
sun.mass = Mstar
sun.radius = 2. | units.AU
sun.x = 0. | units.AU
sun.y = 0. | units.AU
sun.z = 0. | units.AU
sun.vx = 0. | units.kms
sun.vy = 0. | units.kms
sun.vz = 0. | units.kms
def main(Mstar = 1|units.MSun,
Ndisk=100, Mdisk=0.9|units.MSun,
Rmin=1.0|units.AU, Rmax=100.0|units.AU,
Mbump=0.1|units.MSun,Rbump=10.0|units.AU, abump=10|units.AU,
t_end=1, n_steps=10):
converter=nbody_system.nbody_to_si(Mdisk, Rmin)
from amuse.ext.protodisk import ProtoPlanetaryDisk
bodies = ProtoPlanetaryDisk(Ndisk, convert_nbody=converter,
densitypower=1.5, Rmin=1.0,
Rmax=Rmax/Rmin, q_out=1.0,
discfraction=1.0).result
Mdisk = bodies.mass.sum()
bodies.move_to_center()
com = bodies.center_of_mass()
mm = Mdisk/float(Ndisk)
Nbump = Mbump/mm
bump = new_plummer_gas_model(Nbump, convert_nbody=nbody_system.nbody_to_si(Mbump, Rbump))
bump.x += abump
r_bump = abump
inner_particles = bodies.select(lambda r: (com-r).length()<abump,["position"])
M_inner = inner_particles.mass.sum() + Mstar
v_circ = (constants.G*M_inner*(2./r_bump - 1./abump)).sqrt().value_in(units.kms)
bump.velocity += [0, v_circ, 0] | units.kms
bodies.add_particles(bump)
star=Particles(1)
star.mass=Mstar
star.radius= Rmin
star.position = [0, 0, 0] | units.AU
star.velocity = [0, 0, 0] | units.kms
import math
P_bump = (abump**3*4*math.pi**2/(constants.G*(Mbump+Mstar))).sqrt()
t_end *= P_bump
hydro = Gadget2(converter)
hydro.gas_particles.add_particles(bodies)
hydro.dm_particles.add_particles(star)
Etot_init = hydro.kinetic_energy + hydro.potential_energy + hydro.thermal_energy
particles = ParticlesSuperset([star, bodies])
particles.move_to_center()
particles.new_channel_to(hydro.particles).copy()
bodies.h_smooth = Rmin # for the plotting routine
channel_to_star = hydro.dm_particles.new_channel_to(star)
channel_to_bodies = hydro.gas_particles.new_channel_to(bodies)
write_set_to_file(star, "stars.hdf5","hdf5")
write_set_to_file(bodies, "hydro.hdf5","hdf5")
time = 0.0 | t_end.unit
dt = t_end/float(n_steps)
while time < t_end:
time += dt
hydro.evolve_model(time)
channel_to_star.copy()
channel_to_bodies.copy()
write_set_to_file(star, "stars.hdf5","hdf5")
write_set_to_file(bodies, "hydro.hdf5","hdf5")
star.radius = Rmin
from hydro_sink_particles import hydro_sink_particles
lost = hydro_sink_particles(star, bodies)
if len(lost)>0:
hydro.particles.remove_particles(lost)
hydro.particles.synchronize_to(particles)
print "Disk=", hydro.model_time, len(bodies), len(lost), lost.mass.sum(), star.mass
Ekin = hydro.kinetic_energy
Epot = hydro.potential_energy
Eth = hydro.thermal_energy
Etot = Ekin + Epot + Eth
print "T=", hydro.get_time(), "M=", hydro.gas_particles.mass.sum(),
print "E= ", Etot, "Q= ", (Ekin+Eth)/Epot, "dE=", (Etot_init-Etot)/Etot
print "Star=", hydro.model_time, star[0].mass, star[0].position
hydro.stop()
def disk_in_cluster(N_stars, N_gasParticles, W0):
#set up protoplanetary disk
Mdisk = 1.|units.MSun
Rdisk = 100.|units.AU # HD 106906 b is at 700 AU
Rmin, Rmax = 1.|units.AU, Rdisk
converter_disk = nbody_system.nbody_to_si(Mdisk, Rdisk)
disk_particles = ProtoPlanetaryDisk(N_gasParticles, convert_nbody=converter_disk, densitypower=1.5, Rmin=Rmin.value_in(units.AU), Rmax=Rmax.value_in(units.AU), q_out=1.0, discfraction=1.0).result
hydro = Fi(converter_disk, mode='openmp')
hydro.gas_particles.add_particles(disk_particles)
hydro_to_framework = hydro.gas_particles.new_channel_to(disk_particles)
framework_to_hydro = disk_particles.new_channel_to(hydro.gas_particles)
#set up star cluster
Mmin, Mmax = 0.1|units.MSun, 100.|units.MSun
Rvir = 1.|units.parsec
masses = new_kroupa_mass_distribution(N_stars, Mmax)
Mtot_init = masses.sum()
converter_cluster = nbody_system.nbody_to_si(Mtot_init, Rvir)
stars = new_king_model(N_stars, W0, convert_nbody=converter_cluster)
stars.mass = masses
dist_diff = 100. #|units.parsec
magic_index = -1
#put the disk around star closest to 1 solar mass
for i, star in enumerate(stars):
star_x = star.position.value_in(units.parsec)[0]
star_y = star.position.value_in(units.parsec)[1]
star_z = star.position.value_in(units.parsec)[2]
star_dist = np.sqrt(star_x**2 + star_y**2 + star_z**2)
i_diff = np.abs(star_dist - 1.0)
if i_diff < dist_diff:
magic_index = i
dist_diff = i_diff
for gas_particle in disk_particles:
gas_particle.position += stars[magic_index].position
gravitating_bodies = ParticlesSuperset([stars, disk_particles])
gravity = Hermite(converter_cluster)
gravity.particles.add_particles(gravitating_bodies)
gravity_to_framework = gravity.particles.new_channel_to(gravitating_bodies)
framework_to_gravity = gravitating_bodies.new_channel_to(gravity.particles)
combined = bridge.Bridge()
combined.add_system(gravity, (hydro,))
combined.add_system(hydro, (gravity,))
tend, dt = 10.|units.Myr, 0.005|units.Myr
sim_times_unitless = np.arange(0., tend.value_in(units.Myr)+dt.value_in(units.Myr), dt.value_in(units.Myr))
sim_times = [ t|units.Myr for t in sim_times_unitless ]
plt.rc('font', family = 'serif')
cmap = cm.get_cmap('nipy_spectral')
rvals, zvals = [], []
t0 = time.time()
for j, t in enumerate(sim_times):
if j%1 == 0:
print('')
print('simulation time: ', t)
print('wall time: %.03f minutes'%((time.time()-t0)/60.))
stars = gravity.particles[:N_stars]
gas = gravity.particles[N_stars:]
stars_x = [ stars.position[i].value_in(units.parsec)[0] for i in range(len(stars)) ]
stars_y = [ stars.position[i].value_in(units.parsec)[1] for i in range(len(stars)) ]
gas_x = [ gas.position[i].value_in(units.parsec)[0] for i in range(len(gas)) ]
gas_y = [ gas.position[i].value_in(units.parsec)[1] for i in range(len(gas)) ]
plt.figure()
colors = np.log10(stars.mass.value_in(units.MSun))
sc = plt.scatter(stars_x, stars_y, c=colors, s=1, alpha=0.5, label='Stars')
gas_sc = plt.scatter(gas_x, gas_y, c='r', s=1, alpha=0.8, label='Protoplanetary Disk')
cbar = plt.colorbar(sc)
cbar.set_label(r'$\log_{10}(M_{\star}/M_{\odot})$', fontsize=14)
plt.annotate(r'$M_{\mathrm{cluster}} = %.03f \, M_{\odot}$'%(Mtot_init.value_in(units.MSun)), xy=(0.65, 0.15), xycoords='axes fraction', fontsize=8)
plt.annotate(r'$t = %.02f$ Myr'%(t.value_in(units.Myr)), xy=(0.65, 0.1), xycoords='axes fraction', fontsize=8)
plt.xlim(-4.*Rvir.value_in(units.parsec), 4.*Rvir.value_in(units.parsec))
plt.ylim(-4.*Rvir.value_in(units.parsec), 4.*Rvir.value_in(units.parsec))
plt.gca().set_aspect('equal')
plt.xlabel('$x$ (pc)', fontsize=14)
plt.ylabel('$y$ (pc)', fontsize=14)
plt.legend(loc='upper left', fontsize=8)
plt.title(r'King Model, $W_{0} = %.01f$'%(W0), fontsize=14)
plt.savefig('kingmodel_%s.png'%(str(j).rjust(5, '0')))
plt.close()
combined.evolve_model(t)
combined.stop()
return 0