def xtest6(self):
print(
"Test6: Should get error when setting attributes with non-quantities (HDF5 storage)."
)
particles = Particles(4)
particle = Particle()
subset = particles[:2]
superset = ParticlesSuperset([particles, particle.as_set()])
superset.mass = 1.0 | units.MSun
test_results_path = self.get_path_to_results()
output_file = os.path.join(test_results_path, "attr_test.hdf5")
instances = [particles, particle, subset]
classes = [Particles, Particle, ParticlesSubset]
lengths = [4, 1, 2]
for i, x in enumerate(instances):
self.assertTrue(isinstance(x, classes[i]))
self.assertEqual(len(x.as_set()), lengths[i])
if os.path.exists(output_file):
os.remove(output_file)
HDFstorage = store.StoreHDF(output_file)
if isinstance(x, Particle): x = x.as_set()
x.model_time = 2.0 | units.s
HDFstorage.store(x)
loaded_particles = HDFstorage.load()
self.assertRaises(
AttributeError,
self.bogus_func,
loaded_particles,
expected_message=
"Can only assign quantities or other particles to an attribute."
)
HDFstorage.close()
del HDFstorage
def test3(self):
print(
"Test3: Should get error when accessing non-existent attributes (HDF5 storage)."
)
particles = Particles(4)
particle = Particle()
subset = particles[:2]
superset = ParticlesSuperset([particles, particle.as_set()])
superset.mass = 1.0 | units.MSun
test_results_path = self.get_path_to_results()
output_file = os.path.join(test_results_path, "attr_test.hdf5")
instances = [particles, particle, subset]
classes = [Particles, Particle, ParticlesSubset]
lengths = [4, 1, 2]
for i, x in enumerate(instances):
self.assertTrue(isinstance(x, classes[i]))
self.assertEqual(len(x.as_set()), lengths[i])
if os.path.exists(output_file):
os.remove(output_file)
HDFstorage = store.StoreHDF(output_file)
if isinstance(x, Particle): x = x.as_set()
x.model_time = 2.0 | units.s
HDFstorage.store(x)
loaded_particles = HDFstorage.load()
self.assertRaises(
AttributeError,
lambda: loaded_particles.bogus,
expected_message=
"You tried to access attribute 'bogus' but this attribute is not defined for this set."
)
HDFstorage.close()
del HDFstorage
def main(filename="nbody.hdf5", lim=3):
pyplot.ion()
storage = store.StoreHDF(filename, "r")
stars = storage.load()
# lim = 4*stars.center_of_mass().length().value_in(stars.x.unit)
lim = 2 * max(
max(stars.x).value_in(stars.x.unit),
stars.center_of_mass().length().value_in(stars.x.unit))
m = 1 + 3.0 * stars.mass / min(stars.mass)
for si in stars.history:
time = si.get_timestamp()
pyplot.title("Cluster at t=" + str(time))
print "time = ", time
scatter(si.x, si.y, s=m)
xlabel("X")
ylabel("Y")
pyplot.xlim(-lim, lim)
pyplot.ylim(-lim, lim)
pyplot.draw()
pyplot.cla()
pyplot.show()
def simulate_small_cluster(number_of_stars,
end_time=40 | units.Myr,
name_of_the_figure="test-2.svg"):
random.seed()
salpeter_masses = new_salpeter_mass_distribution(number_of_stars)
total_mass = salpeter_masses.sum()
convert_nbody = nbody_system.nbody_to_si(total_mass, 1.0 | units.parsec)
convert_nbody.set_as_default()
particles = new_plummer_model(number_of_stars, convert_nbody)
gravity = PhiGRAPE(convert_nbody, mode="gpu")
gravity.initialize_code()
gravity.parameters.timestep_parameter = 0.01
gravity.parameters.initial_timestep_parameter = 0.01
gravity.parameters.epsilon_squared = 0.000001 | units.parsec**2
stellar_evolution = SSE()
stellar_evolution.initialize_module_with_default_parameters()
#print "setting masses of the stars"
particles.radius = 0.0 | units.RSun
#comment out to get plummer masses
particles.mass = salpeter_masses
gravity.particles.add_particles(particles)
gravity.initialize_particles(0.0)
from_model_to_gravity = particles.new_channel_to(gravity.particles)
from_gravity_to_model = gravity.particles.new_channel_to(particles)
time = 0.0 | units.Myr
particles.savepoint(time)
move_particles_to_center_of_mass(particles)
kineticEnergy = gravity.kinetic_energy.value_in(units.J)
potentialEnergy = gravity.potential_energy.value_in(units.J)
ToverV = kineticEnergy / potentialEnergy
file.write(str(time.value_in(units.Myr)))
file.write(' ')
file.write(str(ToverV))
file.write('\n')
while time < end_time:
time += 0.25 | units.Myr
gravity.evolve_model(time)
from_gravity_to_model.copy()
print "Evolved model to t =", str(time)
print "Evolved model to t =", str(
convert_nbody.to_nbody(time.value_in(units.Myr) | units.Myr))
kineticEnergy = gravity.kinetic_energy.value_in(units.J)
potentialEnergy = gravity.potential_energy.value_in(units.J)
ToverV = kineticEnergy / potentialEnergy
print "Kin / Pot =", ToverV
#print "Particle Mass =", particles[1].mass
file.write(str(time.value_in(units.Myr)))
file.write(' ')
file.write(str(ToverV))
file.write('\n')
file.close()
if os.path.exists('small.hdf5'):
os.remove('small.hdf5')
storage = store.StoreHDF("small.hdf5")
storage.store(particles)
del gravity
del stellar_evolution
def simulate_small_cluster(number_of_stars,
end_time=40 | units.Myr,
name_of_the_figure="test-2.svg"):
# numpy.random.seed(1)
salpeter_masses = new_salpeter_mass_distribution(number_of_stars)
total_mass = salpeter_masses.sum()
convert_nbody = nbody_system.nbody_to_si(total_mass, 1.0 | units.parsec)
particles = new_plummer_model(number_of_stars, convert_nbody)
gravity = BHTree(convert_nbody)
# print gravity.parameters.timestep.as_quantity_in(units.Myr)
gravity.parameters.timestep = 0.0001 | units.Myr # tiny!
gravity.parameters.epsilon_squared \
= (float(number_of_stars)**(-0.333333) | units.parsec) ** 2
stellar_evolution = SSE()
print "setting masses of the stars"
particles.radius = 0.0 | units.RSun
particles.mass = salpeter_masses
print "initializing the particles"
stellar_evolution.particles.add_particles(particles)
from_stellar_evolution_to_model \
= stellar_evolution.particles.new_channel_to(particles)
from_stellar_evolution_to_model.copy_attributes(["mass"])
print "centering the particles"
particles.move_to_center()
print "scaling particles to viridial equilibrium"
particles.scale_to_standard(convert_nbody)
gravity.particles.add_particles(particles)
from_model_to_gravity = particles.new_channel_to(gravity.particles)
from_gravity_to_model = gravity.particles.new_channel_to(particles)
time = 0.0 | units.Myr
particles.savepoint(time)
total_energy_at_t0 = gravity.kinetic_energy + gravity.potential_energy
print "evolving the model until t = " + str(end_time)
while time < end_time:
time += 0.25 | units.Myr
print "gravity evolve step starting"
gravity.evolve_model(time)
print "gravity evolve step done"
print "stellar evolution step starting"
stellar_evolution.evolve_model(time)
print "stellar evolution step done"
from_gravity_to_model.copy()
from_stellar_evolution_to_model.copy_attributes(["mass", "radius"])
particles.savepoint(time)
from_model_to_gravity.copy_attributes(["mass"])
total_energy_at_this_time \
= gravity.kinetic_energy + gravity.potential_energy
print_log(time, gravity, particles, total_energy_at_t0,
total_energy_at_this_time)
test_results_path = get_path_to_results()
output_file = os.path.join(test_results_path, "small.hdf5")
if os.path.exists(output_file):
os.remove(output_file)
storage = store.StoreHDF(output_file)
storage.store(particles)
gravity.stop()
stellar_evolution.stop()
plot_particles(particles, name_of_the_figure)
def validate_bridge():
convert_clu = nbody_system.nbody_to_si(
1.e5 | units.MSun, 1.0 | units.parsec)
convert_gal = nbody_system.nbody_to_si(
1.e7 | units.MSun, 10. | units.parsec)
def convert_gal_to_clu(x): return convert_clu.to_nbody(
convert_gal.to_si(x))
def convert_clu_to_gal(x): return convert_gal.to_nbody(
convert_clu.to_si(x))
total_sim_time = convert_clu_to_gal(200 | nbody_system.time)
total_sim_time = 200 | nbody_system.time
sim_step = 1./128 | nbody_system.time
dt_diag = 1./64 | nbody_system.time
eps_clu = convert_gal_to_clu(2.e-4 | nbody_system.length)
eps_gal = 6.25e-3 | nbody_system.length
cluster = sys_from_king(PhiGRAPE, 1000, 7, convert_clu,
eps_clu, usegl=False, mode="gpu")
galaxy = sys_from_king(Fi, 10000, 9, convert_gal,
eps_gal, sim_step, usegl=False)
shift_sys(
cluster,
convert_clu.to_si(
convert_gal_to_clu(
2.5 | nbody_system.length
)
),
0 | units.m,
0 | units.m,
0 | units.m/units.s,
convert_clu.to_si(
convert_gal_to_clu(0.65 | nbody_system.speed)
),
0 | units.m/units.s)
if hasattr(cluster, "start_viewer"):
cluster.start_viewer()
if hasattr(galaxy, "viewer"):
galaxy.viewer()
clustercopy = copycat(BHTree, cluster, convert_clu)
bridgesys = bridge(verbose=False)
bridgesys.add_system(galaxy, (clustercopy,), False)
bridgesys.add_system(cluster, (galaxy,), True)
t = 0. | nbody_system.time
if os.path.exists("cluster.hdf"):
os.remove("cluster.hdf")
storage = store.StoreHDF("cluster.hdf")
bridgesys.synchronize_model()
Ep0 = bridgesys.potential_energy
Ek0 = bridgesys.kinetic_energy
Esp0 = cluster.kinetic_energy
Esk0 = cluster.potential_energy
tc = cluster.model_time
tg = galaxy.model_time
print(convert_gal.to_nbody(tg))
print(0.)
# print Ep0,Ek0
# print Esp0,Esk0
for x in cluster.get_center_of_mass_position():
print(convert_gal.to_nbody(x), end=' ')
print()
part = bridgesys.particles.copy()
part.savepoint(tg)
storage.store(part.previous_state())
while(t < total_sim_time):
t = t+dt_diag
bridgesys.evolve_model(convert_gal.to_si(t),
timestep=convert_gal.to_si(sim_step))
bridgesys.synchronize_model()
Ep = bridgesys.potential_energy
Ek = bridgesys.kinetic_energy
Esp = cluster.kinetic_energy
Esk = cluster.potential_energy
tc = cluster.model_time
tg = galaxy.model_time
print(convert_gal.to_nbody(tg))
print((Ep+Ek-Ep0-Ek0)/(Ep0+Ek0))
# print (Esp+Esk-Esp0-Esk0)/(Esp0+Esk0)
for x in cluster.get_center_of_mass_position():
print(convert_gal.to_nbody(x), end=' ')
print()
part = bridgesys.particles.copy()
part.savepoint(tg)
storage.store(part.previous_state())
def simulate_small_cluster(number_of_stars,
end_time=40 | units.Myr,
name_of_the_figure="test-2.svg"):
random.seed()
salpeter_masses = new_salpeter_mass_distribution(number_of_stars)
total_mass = salpeter_masses.sum()
convert_nbody = nbody_system.nbody_to_si(total_mass, 1.0 | units.parsec)
convert_nbody.set_as_default()
print 'end_time:', convert_nbody.to_nbody(end_time)
print convert_nbody.to_nbody(total_mass)
particles = new_plummer_model(number_of_stars, convert_nbody)
gravity = PhiGRAPE(convert_nbody, mode="gpu", use_gl="true")
gravity.parameters.timestep_parameter = 0.01
gravity.parameters.initial_timestep_parameter = 0.01
gravity.parameters.epsilon_squared = 0.0015 | units.parsec**2
particles.radius = 0.0 | units.RSun
# particles.mass = salpeter_masses
move_particles_to_center_of_mass(particles)
gravity.particles.add_particles(particles)
gravity.initialize_particles(0.0)
gravity.start_viewer()
from_model_to_gravity = particles.new_channel_to(gravity.particles)
from_gravity_to_model = gravity.particles.new_channel_to(particles)
time = 0.0 | units.Myr
# particles.savepoint(time)
kineticEnergy = gravity.kinetic_energy.value_in(units.J)
potentialEnergy = gravity.potential_energy.value_in(units.J)
ToverV = kineticEnergy / potentialEnergy
E0 = convert_nbody.to_nbody(gravity.kinetic_energy +
gravity.potential_energy)
file.write(str(time.value_in(units.Myr)))
file.write(' ')
file.write(str(ToverV))
file.write('\n')
gravity.parameters.timestep_parameter = 0.01
gravity.parameters.initial_timestep_parameter = 0.01
while time < end_time:
time += 0.5 * convert_nbody.to_si(1 | nbody_system.time)
gravity.evolve_model(time)
gravity.synchronize_model()
from_gravity_to_model.copy()
print "Evolved model to t =", str(time)
kineticEnergy = gravity.kinetic_energy.value_in(units.J)
potentialEnergy = gravity.potential_energy.value_in(units.J)
ToverV = kineticEnergy / potentialEnergy
Et = convert_nbody.to_nbody(gravity.kinetic_energy +
gravity.potential_energy)
print "Kin / Pot =", ToverV, (Et - E0) / E0
file.write(str(time.value_in(units.Myr)))
file.write(' ')
file.write(str(ToverV))
file.write('\n')
file.close()
if os.path.exists('small.hdf5'):
os.remove('small.hdf5')
storage = store.StoreHDF("small.hdf5")
storage.store(particles)
del gravity
del stellar_evolution
