def test1(self):
print("Test 1: initialization")
instance = SimpleXSplitSet(**default_options)
instance.initialize_code()
instance.commit_parameters()
instance.cleanup_code()
instance.stop()
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 test1(self):
print "Test 1: initialization"
instance = SimpleXSplitSet(**default_options)
instance.initialize_code()
instance.commit_parameters()
instance.cleanup_code()
instance.stop()
def irradiate_disk_with_bump(Mstar=10 | units.MSun,
tstar=20 | units.Myr,
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=10 | units.yr,
n_steps=10):
dt = t_end / float(n_steps)
stellar = SeBa()
stellar.particles.add_particle(Particle(mass=Mstar))
stellar.evolve_model(tstar)
source = Particles(1)
source.mass = stellar.particles[0].mass
source.position = (0, 0, 0) | units.AU
source.velocity = (0, 0, 0) | units.kms
source.luminosity = stellar.particles[0].luminosity / (20. | units.eV)
source.temperature = stellar.particles[0].temperature
Teff = stellar.particles[0].temperature
source.flux = source.luminosity
source.rho = 1.0 | (units.g / units.cm**3)
source.xion = 0.0 #ionization_fraction
source.u = (9. | units.kms)**2 #internal_energy
stellar.stop()
ism = new_disk_with_bump(source[0].mass, Ndisk, Mdisk, Rmin, Rmax, Mbump,
Rbump, abump)
ism.flux = 0 | units.s**-1
ism.xion = 0.0 #ionization_fraction
hydro = Gadget2(nbody_system.nbody_to_si(Mdisk, Rmax))
hydro.gas_particles.add_particles(ism)
hydro.dm_particles.add_particles(source)
hydro.evolve_model(1 | units.day)
hydro.gas_particles.new_channel_to(ism).copy()
hydro.stop()
rad = SimpleXSplitSet(redirect="none", numer_of_workers=4)
rad.parameters.box_size = 2.01 * Rmax
rad.parameters.timestep = 0.1 * dt
rad.set_source_Teff(Teff)
rad.src_particles.add_particle(source)
rad.gas_particles.add_particles(ism)
rad_to_framework = rad.gas_particles.new_channel_to(ism)
particles = ParticlesSuperset([source, ism])
write_set_to_file(particles, "rad.hdf5", 'hdf5')
while rad.model_time < t_end:
rad.evolve_model(rad.model_time + dt)
rad_to_framework.copy_attributes(["x", "y", "z", "xion"])
write_set_to_file(particles, "rad.hdf5", 'hdf5')
print "Time=", rad.model_time, "Ionization (min, mean, max):", ism.xion.min(
), ism.xion.mean(), ism.xion.max()
rad.stop()
def irradiate_disk_with_bump(Mstar = 10|units.MSun, tstar = 20|units.Myr,
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=10|units.yr, n_steps=10,
filename = None, image_id=1):
dt = t_end/float(n_steps)
stellar = SeBa()
stellar.particles.add_particle(Particle(mass=Mstar))
stellar.evolve_model(tstar)
source=Particles(1)
source.mass = stellar.particles[0].mass
source.position = (0, 0, 0) |units.AU
source.velocity = (0, 0, 0) |units.kms
source.luminosity = stellar.particles[0].luminosity/(20. | units.eV)
source.temperature = stellar.particles[0].temperature
Teff = stellar.particles[0].temperature
source.flux = source.luminosity
source.rho = 1.0|(units.g/units.cm**3)
source.xion = 0.0 #ionization_fraction
source.u = (9. |units.kms)**2 #internal_energy
stellar.stop()
ism = new_disk_with_bump(source[0].mass, Ndisk, Mdisk, Rmin, Rmax,
Mbump, Rbump, abump)
ism.flux = 0 | units.s**-1
ism.xion = 0.0 #ionization_fraction
hydro = Gadget2(nbody_system.nbody_to_si(Mdisk, Rmax))
hydro.gas_particles.add_particles(ism)
hydro.dm_particles.add_particles(source)
hydro.evolve_model(1|units.day)
hydro.gas_particles.new_channel_to(ism).copy()
hydro.stop()
rad = SimpleXSplitSet(redirect="none",numer_of_workers=4)
rad.parameters.box_size=2.01*Rmax
rad.parameters.timestep=0.1*dt
rad.set_source_Teff(Teff)
rad.src_particles.add_particle(source)
rad.gas_particles.add_particles(ism)
rad_to_framework = rad.gas_particles.new_channel_to(ism)
particles = ParticlesSuperset([source, ism])
write_set_to_file(particles, "rad.hdf5", 'hdf5')
while rad.model_time<t_end:
rad.evolve_model(rad.model_time + dt)
rad_to_framework.copy_attributes(["x","y", "z", "xion"])
write_set_to_file(particles, "rad.hdf5", 'hdf5')
print "Time=", rad.model_time, "Ionization (min, mean, max):", ism.xion.min(), ism.xion.mean(), ism.xion.max()
rad.stop()
def test4(self):
print("Test 4: default parameters")
instance = SimpleXSplitSet(**default_options)
default = dict(timestep=0.05 | units.Myr,
source_effective_T=1.e5 | units.K,
hilbert_order=1,
number_of_freq_bins=1,
thermal_evolution_flag=0,
blackbody_spectrum_flag=0,
box_size=13200 | units.parsec,
metal_cooling_flag=0,
collisional_ionization_flag=0)
for x in default:
self.assertEqual(getattr(instance.parameters, x), default[x])
instance.commit_parameters()
for x in default:
self.assertEqual(getattr(instance.parameters, x), default[x])
tnow = instance.model_time
self.assertEqual(tnow, 0. | units.Myr)
instance.model_time = 321. | units.Myr
tnow = instance.model_time
self.assertEqual(tnow, 321. | units.Myr)
def test4(self):
print "Test 4: default parameters"
instance = SimpleXSplitSet(**default_options)
default=dict( timestep= 0.05| units.Myr,
source_effective_T= 1.e5 | units.K,
hilbert_order= 1,
number_of_freq_bins= 1,
thermal_evolution_flag = 0,
blackbody_spectrum_flag = 0,
box_size=13200 | units.parsec,
metal_cooling_flag=0,
collisional_ionization_flag=0)
for x in default:
self.assertEqual(getattr(instance.parameters,x), default[x])
instance.commit_parameters()
for x in default:
self.assertEqual(getattr(instance.parameters,x), default[x])
tnow=instance.model_time
self.assertEqual(tnow, 0. | units.Myr)
instance.model_time=321. | units.Myr
tnow=instance.model_time
self.assertEqual(tnow, 321. | units.Myr)
def test5(self):
print("Test 4: default parameters")
instance = SimpleXSplitSet(**default_options)
param = dict(timestep=0.1 | units.Myr,
source_effective_T=2.e5 | units.K,
hilbert_order=3,
number_of_freq_bins=4,
thermal_evolution_flag=1,
blackbody_spectrum_flag=1,
box_size=32100 | units.parsec,
metal_cooling_flag=1,
collisional_ionization_flag=1)
for x in param:
setattr(instance.parameters, x, param[x])
for x in param:
self.assertEqual(getattr(instance.parameters, x), param[x])
def test3(self):
print("Test 3: evolve")
instance = SimpleXSplitSet(**default_options)
instance.initialize_code()
instance.commit_parameters()
input_file = os.path.join(os.path.dirname(__file__),
"test_simplex_data.txt")
particles, src_particles = splitset_from_input_file(input_file)
instance.src_particles.add_particles(src_particles)
particles.du_dt = particles.u / (10 | units.Myr)
instance.gas_particles.add_particles(particles)
self.assertAlmostEqual(instance.gas_particles.xion.mean(), 0.0)
self.assertAlmostEqual(
instance.gas_particles.du_dt.mean().in_(units.cm**2 / units.s**3),
particles.du_dt.mean().in_(units.cm**2 / units.s**3))
self.assertEqual(instance.get_name_of_current_state(), 'EDIT')
instance.evolve_model(0.5 | units.Myr)
self.assertEqual(instance.get_name_of_current_state(), 'RUN')
self.assertAlmostEqual(
instance.gas_particles.du_dt.mean().in_(units.cm**2 / units.s**3),
particles.du_dt.mean().in_(units.cm**2 / units.s**3))
self.assertAlmostEqual(instance.gas_particles.xion.mean(),
0.000845247683257)
instance.gas_particles.remove_particles(particles[0:4])
# this is what we would like....
# self.assertEquals(instance.get_name_of_current_state(), 'UPDATE')
# instance.recommit_particles()
instance.evolve_model(0.75 | units.Myr)
self.assertEqual(len(instance.particles), len(particles) - 4)
instance.cleanup_code()
instance.stop()
def test2(self):
print("Test 2: commit_particles, getters and setters")
instance = SimpleXSplitSet(**default_options)
instance.initialize_code()
instance.commit_parameters()
input_file = os.path.join(os.path.dirname(__file__),
"test_simplex_data.txt")
particles, src_particles = splitset_from_input_file(input_file)
instance.gas_particles.add_particles(particles)
instance.src_particles.add_particles(src_particles)
instance.commit_particles()
# for attribute in ['position', 'rho', 'flux', 'xion']:
# self.assertAlmostEqual(13200.*getattr(particles, attribute),
# 13200.*getattr(instance.particles, attribute), 5)
# setattr(instance.particles, attribute, getattr(particles, attribute)/2.0)
# self.assertAlmostEqual(13200.*getattr(particles, attribute)/2.0,
# 13200.*getattr(instance.particles, attribute), 5)
instance.cleanup_code()
instance.stop()
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 test3(self):
print "Test 3: evolve"
instance = SimpleXSplitSet(**default_options)
instance.initialize_code()
instance.commit_parameters()
input_file = os.path.join(os.path.dirname(__file__), "test_simplex_data.txt")
particles,src_particles = splitset_from_input_file(input_file)
instance.src_particles.add_particles(src_particles)
particles.du_dt = particles.u/(10|units.Myr)
instance.gas_particles.add_particles(particles)
self.assertAlmostEqual(instance.gas_particles.xion.mean(), 0.0)
self.assertAlmostEqual(instance.gas_particles.du_dt.mean().in_(units.cm**2/units.s**3),particles.du_dt.mean().in_(units.cm**2/units.s**3))
self.assertEquals(instance.get_name_of_current_state(), 'EDIT')
instance.evolve_model(0.5 | units.Myr)
self.assertEquals(instance.get_name_of_current_state(), 'RUN')
self.assertAlmostEqual(instance.gas_particles.du_dt.mean().in_(units.cm**2/units.s**3),particles.du_dt.mean().in_(units.cm**2/units.s**3))
self.assertAlmostEqual(instance.gas_particles.xion.mean(), 0.000845247683257)
instance.gas_particles.remove_particles(particles[0:4])
# this is what we would like....
# self.assertEquals(instance.get_name_of_current_state(), 'UPDATE')
# instance.recommit_particles()
instance.evolve_model(0.75 | units.Myr)
self.assertEqual(len(instance.particles), len(particles)-4)
instance.cleanup_code()
instance.stop()
def test2(self):
print "Test 2: commit_particles, getters and setters"
instance = SimpleXSplitSet(**default_options)
instance.initialize_code()
instance.commit_parameters()
input_file = os.path.join(os.path.dirname(__file__), "test_simplex_data.txt")
particles,src_particles = splitset_from_input_file(input_file)
instance.gas_particles.add_particles(particles)
instance.src_particles.add_particles(src_particles)
instance.commit_particles()
# for attribute in ['position', 'rho', 'flux', 'xion']:
# self.assertAlmostEqual(13200.*getattr(particles, attribute),
# 13200.*getattr(instance.particles, attribute), 5)
# setattr(instance.particles, attribute, getattr(particles, attribute)/2.0)
# self.assertAlmostEqual(13200.*getattr(particles, attribute)/2.0,
# 13200.*getattr(instance.particles, attribute), 5)
instance.cleanup_code()
instance.stop()
def _irradiate_disk_with_pump(Mstar = 10|units.MSun,
tstar = 20|units.Myr,
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=10|units.yr, n_steps=10, filename = None, image_id=1):
model_time = 0.0 | t_end.unit
dt = t_end/float(n_steps)
ionization_fraction = 0.0
internal_energy = (9. |units.kms)**2
stellar = SeBa()
stellar.particles.add_particle(Particle(mass=Mstar))
stellar.evolve_model(tstar)
print "L=", stellar.particles[0].luminosity.in_(units.LSun), stellar.particles[0].temperature
source=Particles(1)
source.mass = stellar.particles[0].mass
source.position = (0, 0, 0) |units.AU
source.velocity = (0, 0, 0) |units.kms
source.luminosity = stellar.particles[0].luminosity/(20. | units.eV)
source.temperature = stellar.particles[0].temperature
Teff = stellar.particles[0].temperature
source.flux = source.luminosity
source.rho = 1.0|(units.g/units.cm**3)
source.xion = ionization_fraction
source.u = internal_energy
stellar.stop()
Mstar = source[0].mass
if filename ==None:
ism = new_disk_with_bump(Mstar = Mstar,
Ndisk=Ndisk, Mdisk=Mdisk,
Rmin=Rmin, Rmax=Rmax,
Mbump=Mbump, Rbump=Rbump,
abump=abump)
else:
ism = read_disk_with_bump(image_id=image_id, filename=filename)#, Rmax=Rmax)
ism = ism.select(lambda r: r.length()<1.0*Rmax,["position"])
ism.flux = 0 | units.s**-1
ism.xion = ionization_fraction
if filename ==None:
converter=nbody_system.nbody_to_si(Mdisk, Rmax)
hydro = Gadget2(converter)
hydro.gas_particles.add_particles(ism)
hydro.dm_particles.add_particles(source)
hydro.evolve_model(1|units.day)
hydro.gas_particles.new_channel_to(ism).copy()
hydro.stop()
rad = SimpleXSplitSet(redirect="none",numer_of_workers=4)
rad.parameters.number_of_freq_bins=5
rad.parameters.thermal_evolution_flag=1
rad.parameters.blackbody_spectrum_flag=1
rad.parameters.metal_cooling_flag=0
rad.parameters.box_size=2.01*Rmax
if isinstance(rad, SPHRay):
ism.h_smooth = 0.1 | (units.RSun)
else:
rad.parameters.timestep=0.1*dt
rad.set_source_Teff(Teff)
rad.src_particles.add_particle(source)
rad.gas_particles.add_particles(ism)
channel_from_rad_to_framework = rad.gas_particles.new_channel_to(ism)
particles = ParticlesSuperset([source, ism])
write_set_to_file(particles, "rad.hdf5", 'hdf5')
tCPU = time()
while model_time<t_end:
model_time += dt
rad.evolve_model(model_time)
channel_from_rad_to_framework.copy_attributes(["x","y", "z", "xion"])
write_set_to_file(particles, "rad.hdf5", 'hdf5')
print "Date:"+str(localtime()[2])+"."+str(localtime()[1])+"."+str(localtime()[1]), "at", str(localtime()[3])+"h", str(localtime()[4])+"m"
print "Time=", model_time, "dt_CPU=", time()-tCPU
print "min ionization:", ism.xion.min()
print "average Xion:", ism.xion.mean()
print "max ionization:", ism.xion.max()
tCPU = time()
rad.stop()