def result(self):
self.setup_lookup_tables()
self.setup_variates()
sph_particles = Particles(self.number_of_sph_particles)
sph_particles.position = self.new_particle_positions()
sph_particles.velocity = self.new_particle_velocities()
sph_particles.u = self.new_particle_specific_internal_energies()
sph_particles.rho = self.new_particle_densities()
sph_particles.mass = (self.mass.number * 1.0 / self.number_of_sph_particles) | self.mass.unit
# Crude estimate of the smoothing length; the SPH code will calculate the true value itself.
sph_particles.h_smooth = (self.grid.get_volume() * 50.0/self.number_of_sph_particles)**(1/3.0)
return sph_particles
def setup_sph_code(self, sph_code, number_of_particles, L, rho, u):
converter = ConvertBetweenGenericAndSiUnits(L, rho, constants.G)
sph_code = sph_code(converter, mode = 'periodic')#, redirection = 'none')
sph_code.parameters.periodic_box_size = 10.0 | units.parsec
gas = Particles(number_of_particles)
gas.mass = (rho * L**3) / number_of_particles
numpy.random.seed(12345)
gas.x = L * numpy.random.uniform(0.0, 1.0, number_of_particles)
gas.y = L * numpy.random.uniform(0.0, 1.0, number_of_particles)
gas.z = L * numpy.random.uniform(0.0, 1.0, number_of_particles)
gas.vx = numpy.zeros(number_of_particles) | units.cm / units.s
gas.vy = numpy.zeros(number_of_particles) | units.cm / units.s
gas.vz = numpy.zeros(number_of_particles) | units.cm / units.s
gas.u = u
if isinstance(sph_code, Fi):
sph_code.parameters.self_gravity_flag = False
sph_code.parameters.timestep = 0.1 | generic_unit_system.time
gas.h_smooth = L / number_of_particles**(1/3.0)
gas.position -= 0.5 * L
sph_code.gas_particles.add_particles(gas)
sph_code.commit_particles()
#~ sph_code.evolve_model(0.01 | units.Myr)
return sph_code
def res_increase(
gas=None,
recalculate_h_density=False,
seed=123,
make_cutout=False,
make_circular_cutout=False,
circular_rmax=3000 | units.pc,
x_center=None,
y_center=None,
width=None,
res_increase_factor=85,
):
numpy.random.seed(seed)
if gas is None:
if len(sys.argv) > 2:
from amuse.io import read_set_from_file
filename = sys.argv[1]
res_increase_factor = int(sys.argv[2])
gas = read_set_from_file(filename, 'amuse')
if hasattr(gas, "itype"):
gas = gas[gas.itype == 1]
del gas.itype
else:
from amuse.ic.gasplummer import new_plummer_gas_model
converter = nbody_system.nbody_to_si(10000 | units.MSun,
10 | units.pc)
filename = "test"
gas = new_plummer_gas_model(10000, converter)
res_increase_factor = 85
sph = Fi(converter, mode="openmp")
gas_in_code = sph.gas_particles.add_particles(gas)
gas.h_smooth = gas_in_code.h_smooth
gas.density = gas_in_code.density
sph.stop()
write_set_to_file(gas, "old-%s" % filename, "amuse")
print("old gas created")
if make_circular_cutout:
r2 = gas.x**2 + gas.y**2
cutout = gas[r2 <= circular_rmax**2]
gas = cutout
converter = nbody_system.nbody_to_si(gas.total_mass(), width)
sph = Fi(converter, mode="openmp")
gas_in_code = sph.gas_particles.add_particles(gas)
gas.h_smooth = gas_in_code.h_smooth
gas.density = gas_in_code.density
sph.stop()
if make_cutout:
if (x_center is None or y_center is None or width is None):
raise Exception("Need to set x_center, y_center and width!")
cutout = gas.sorted_by_attribute("x")
cutout = cutout[cutout.x - x_center < width / 2]
cutout = cutout[cutout.x - x_center > -width / 2]
cutout = cutout.sorted_by_attribute("y")
cutout = cutout[cutout.y - y_center < width / 2]
cutout = cutout[cutout.y - y_center > -width / 2]
gas = cutout
converter = nbody_system.nbody_to_si(gas.total_mass(), width)
sph = Fi(converter, mode="openmp")
gas_in_code = sph.gas_particles.add_particles(gas)
gas.h_smooth = gas_in_code.h_smooth
gas.density = gas_in_code.density
sph.stop()
# boundary = test_cutout.h_smooth.max()
if res_increase_factor == 1:
return gas
original_number_of_particles = len(gas)
new_number_of_particles = (res_increase_factor *
original_number_of_particles)
converter = nbody_system.nbody_to_si(
gas.total_mass(),
1 | units.kpc,
)
new_gas = Particles(new_number_of_particles)
# new_gas.h_smooth = gas.h_smooth
shells, particles_per_shell, shell_radii = find_shell_struct(
res_increase_factor)
relative_positions = pos_shift(
shell_radii,
particles_per_shell,
res_increase_factor=res_increase_factor,
)
relative_velocities = numpy.zeros(
res_increase_factor * 3, dtype=float).reshape(res_increase_factor,
3) | gas.velocity.unit
random_samples = 50
number_of_particles = len(gas)
starting_index = 0
for r in range(random_samples):
print("%i / %i random sample done" % (r, random_samples))
number_of_particles_remaining = len(gas)
number_of_particles_in_sample = min(
number_of_particles_remaining,
int(1 + number_of_particles / random_samples))
gas_sample = gas.random_sample(number_of_particles_in_sample).copy()
gas.remove_particles(gas_sample)
end_index = (starting_index +
number_of_particles_in_sample * res_increase_factor)
new_gas_sample = new_gas[starting_index:end_index]
psi = 2 * numpy.pi * numpy.random.random()
theta = 2 * numpy.pi * numpy.random.random()
phi = 2 * numpy.pi * numpy.random.random()
relative_positions = rotated(relative_positions, phi, theta, psi)
# print(len(gas_sample), len(new_gas_sample))
for i in range(res_increase_factor):
new_gas_sample[i::res_increase_factor].mass = (gas_sample.mass /
res_increase_factor)
new_gas_sample[i::res_increase_factor].x = (
gas_sample.x + relative_positions[i, 0] * gas_sample.h_smooth)
new_gas_sample[i::res_increase_factor].y = (
gas_sample.y + relative_positions[i, 1] * gas_sample.h_smooth)
new_gas_sample[i::res_increase_factor].z = (
gas_sample.z + relative_positions[i, 2] * gas_sample.h_smooth)
new_gas_sample[i::res_increase_factor].vx = (
gas_sample.vx + relative_velocities[i, 0])
new_gas_sample[i::res_increase_factor].vy = (
gas_sample.vy + relative_velocities[i, 1])
new_gas_sample[i::res_increase_factor].vz = (
gas_sample.vz + relative_velocities[i, 2])
new_gas_sample[i::res_increase_factor].density = gas_sample.density
new_gas_sample[i::res_increase_factor].u = gas_sample.u
starting_index += number_of_particles_in_sample * res_increase_factor
new_gas.h_smooth = ((3 * new_gas.mass / (4 * pi * new_gas.density))**(1 /
3))
# sph = Fi(converter, mode="openmp", redirection="none")
# new_gas_in_code = sph.gas_particles.add_particles(new_gas)
# new_gas.h_smooth = new_gas_in_code.h_smooth
# new_gas.density = new_gas_in_code.density
# sph.stop()
print("particles now have a mass of %s" %
(new_gas[0].mass.in_(units.MSun)))
return new_gas
def make_xyz(self):
from amuse.community.fi.interface import Fi
N = self.targetN
target_rms = self.target_rms
L = 1 | nbody_system.length
dt = 0.01 | nbody_system.time
x, y, z = uniform_random_unit_cube(N).make_xyz()
vx, vy, vz = uniform_unit_sphere(N).make_xyz()
p = Particles(N)
p.x = L * x
p.y = L * y
p.z = L * z
p.h_smooth = 0. * L
p.vx = 0.1 * vx | (nbody_system.speed)
p.vy = 0.1 * vy | (nbody_system.speed)
p.vz = 0.1 * vz | (nbody_system.speed)
p.u = (0.1 * 0.1) | nbody_system.speed**2
p.mass = (8. / N) | nbody_system.mass
sph = Fi(use_gl=False, mode='periodic', redirection='none')
sph.initialize_code()
sph.parameters.use_hydro_flag = True
sph.parameters.radiation_flag = False
sph.parameters.self_gravity_flag = False
sph.parameters.gamma = 1.
sph.parameters.isothermal_flag = True
sph.parameters.integrate_entropy_flag = False
sph.parameters.timestep = dt
sph.parameters.verbosity = 0
sph.parameters.periodic_box_size = 2 * L
sph.parameters.artificial_viscosity_alpha = 1.
sph.parameters.beta = 2.
sph.commit_parameters()
sph.gas_particles.add_particles(p)
sph.commit_particles()
# sph.start_viewer()
t = 0. | nbody_system.time
rms = 1.
minrms = 1.
i = 0
while rms > target_rms:
i += 1
t = t + (0.25 | nbody_system.time)
sph.evolve_model(t)
rho = sph.particles.rho.value_in(nbody_system.density)
rms = rho.std() / rho.mean()
minrms = min(minrms, rms)
if rms > 2. * minrms or i > 300:
print " RMS(rho) convergence warning:", i, rms, minrms
if i > 100000:
print "i> 100k steps - not sure about this..."
print " rms:", rms
break
x = sph.particles.x.value_in(nbody_system.length)
y = sph.particles.y.value_in(nbody_system.length)
z = sph.particles.z.value_in(nbody_system.length)
del sph
return x, y, z
def glass(self):
from amuse.community.fi.interface import Fi
if self.target_rms < 0.0001:
print "warning: target_rms may not succeed"
if self.number_of_particles < 1000:
print "warning: not enough particles"
N = 2 * self.number_of_particles
L = 1 | nbody_system.length
dt = 0.01 | nbody_system.time
x, y, z = self._random_cube(N)
vx,vy,vz= self.random(N)
p = Particles(N)
p.x = L * x
p.y = L * y
p.z = L * z
p.h_smooth = 0.0 | nbody_system.length
p.vx = (0.1 | nbody_system.speed) * vx
p.vy = (0.1 | nbody_system.speed) * vy
p.vz = (0.1 | nbody_system.speed) * vz
p.u = (0.1*0.1) | nbody_system.speed**2
p.mass = (8.0/N) | nbody_system.mass
sph = Fi(mode = 'periodic', redirection = 'none')
sph.initialize_code()
sph.parameters.use_hydro_flag = True
sph.parameters.radiation_flag = False
sph.parameters.self_gravity_flag = False
sph.parameters.gamma = 1.0
sph.parameters.isothermal_flag = True
sph.parameters.integrate_entropy_flag = False
sph.parameters.timestep = dt
sph.parameters.verbosity = 0
sph.parameters.periodic_box_size = 2 * L
sph.parameters.artificial_viscosity_alpha = 1.0
sph.parameters.beta = 2.0
sph.commit_parameters()
sph.gas_particles.add_particles(p)
sph.commit_particles()
t = 0.0 | nbody_system.time
rms = 1.0
minrms = 1.0
i = 0
while rms > self.target_rms:
i += 1
t += (0.25 | nbody_system.time)
sph.evolve_model(t)
rho = sph.particles.rho.value_in(nbody_system.density)
rms = rho.std()/rho.mean()
minrms = min(minrms, rms)
if (rms > 2.0*minrms) or (i > 300):
print " RMS(rho) convergence warning:", i, rms, minrms
if i > 100000:
print "i> 100k steps - not sure about this..."
print " rms:", rms
break
x = sph.particles.x.value_in(nbody_system.length)
y = sph.particles.y.value_in(nbody_system.length)
z = sph.particles.z.value_in(nbody_system.length)
sph.stop()
del sph
return self._cutout_sphere(x, y, z)
def glass(self):
from amuse.community.fi.interface import Fi
if self.target_rms < 0.0001:
print("warning: target_rms may not succeed")
if self.number_of_particles < 1000:
print("warning: not enough particles")
N = 2 * self.number_of_particles
L = 1 | nbody_system.length
dt = 0.01 | nbody_system.time
x, y, z = self._random_cube(N)
vx,vy,vz= self.random(N)
p = Particles(N)
p.x = L * x
p.y = L * y
p.z = L * z
p.h_smooth = 0.0 | nbody_system.length
p.vx = (0.1 | nbody_system.speed) * vx[:N]
p.vy = (0.1 | nbody_system.speed) * vy[:N]
p.vz = (0.1 | nbody_system.speed) * vz[:N]
p.u = (0.1*0.1) | nbody_system.speed**2
p.mass = (8.0/N) | nbody_system.mass
sph = Fi(mode = 'periodic', redirection = 'none')
sph.initialize_code()
sph.parameters.use_hydro_flag = True
sph.parameters.radiation_flag = False
sph.parameters.self_gravity_flag = False
sph.parameters.gamma = 1.0
sph.parameters.isothermal_flag = True
sph.parameters.integrate_entropy_flag = False
sph.parameters.timestep = dt
sph.parameters.verbosity = 0
sph.parameters.periodic_box_size = 2 * L
sph.parameters.artificial_viscosity_alpha = 1.0
sph.parameters.beta = 2.0
sph.commit_parameters()
sph.gas_particles.add_particles(p)
sph.commit_particles()
t = 0.0 | nbody_system.time
rms = 1.0
minrms = 1.0
i = 0
while rms > self.target_rms:
i += 1
t += (0.25 | nbody_system.time)
sph.evolve_model(t)
rho = sph.particles.rho.value_in(nbody_system.density)
rms = rho.std()/rho.mean()
minrms = min(minrms, rms)
if (rms > 2.0*minrms) or (i > 300):
print(" RMS(rho) convergence warning:", i, rms, minrms)
if i > 100000:
print("i> 100k steps - not sure about this...")
print(" rms:", rms)
break
x = sph.particles.x.value_in(nbody_system.length)
y = sph.particles.y.value_in(nbody_system.length)
z = sph.particles.z.value_in(nbody_system.length)
sph.stop()
del sph
return self._cutout_sphere(x, y, z)
def iliev_test_7_ic(N=10000, Ns=10, L=6.6 | units.kpc):
print "Initializing iliev_test_7"
mp = rhoinit * (2 * L)**3 / N
Nc = ((rhoclump * 4 * constants.pi / 3 * (0.8 | units.kpc)**3) / mp)
Nc = int(Nc)
print Nc
try:
f = open("glass%9.9i.pkl" % N, "rb")
x, y, z = cPickle.load(f)
f.close()
except:
x, y, z = glass_unit_cube(N, target_rms=0.05).make_xyz()
f = open("glass%9.9i.pkl" % N, "wb")
cPickle.dump((x, y, z), f)
f.close()
sel = numpy.where(((x -
(5. / 6.6))**2 + y**2 + z**2)**0.5 > (0.8 / 6.6))[0]
x = x[sel]
y = y[sel]
z = z[sel]
p = Particles(len(x))
print len(x)
# set particles homogeneously in space
p.x = L * x
p.y = L * y
p.z = L * z
# set other properties
p.h_smooth = 0. | units.parsec
p.vx = 0. | (units.km / units.s)
p.vy = 0. | (units.km / units.s)
p.vz = 0. | (units.km / units.s)
p.u = uinit
p.rho = rhoinit
p.mass = mp
p.flux = 0. | (units.s**-1)
p.xion = 0. | units.none
sources = Particles(Ns)
x, y, z = uniform_unit_sphere(Ns).make_xyz()
if Ns == 1:
x, y, z = 0., 0., 0.
sources.x = -(5. | units.kpc) + L * x * (1. / N)**(1. / 3) / 10
sources.y = L * y * (1. / N)**(1. / 3) / 10
sources.z = L * z * (1. / N)**(1. / 3) / 10
sources.luminosity = (1.2e52 / Ns) | (units.s**-1)
sources.SpcType = 1.
clump = Particles(Nc)
x, y, z = uniform_unit_sphere(Nc).make_xyz()
clump.x = (5. | units.kpc) + (0.8 | units.kpc) * x
clump.y = (0.8 | units.kpc) * y
clump.z = (0.8 | units.kpc) * z
clump.h_smooth = 0. | units.parsec
clump.vx = 0. | (units.km / units.s)
clump.vy = 0. | (units.km / units.s)
clump.vz = 0. | (units.km / units.s)
clump.u = uclump
clump.rho = rhoclump
clump.mass = mp
clump.flux = 0. | (units.s**-1)
clump.xion = 0. | units.none
p.add_particles(clump)
return p, sources
def set_gas_and_src(Ngas, Lbox, Lsrc, rho_init, T_init):
""" Given the number of particles and box parameters, sets up gas
particles and a source particle. """
gamma = 5. / 3.
mu = 1.0 | units.amu
# set particles homogeneously in space from -Lbox/2 to Lbox/2
# NOTE reset Ngas
if args.grid == 1:
x, y, z = regular_grid_unit_cube(Ngas).make_xyz()
#x,y,z = body_centered_grid_unit_cube(Ngas).make_xyz()
Ngas = len(x)
gas = Particles(Ngas)
gas.x = x * Lbox / 2
gas.y = y * Lbox / 2
gas.z = z * Lbox / 2
elif args.grid == 0:
gas = Particles(Ngas)
gas.x = Lbox / 2 * numpy.random.uniform(-1., 1., Ngas)
gas.y = Lbox / 2 * numpy.random.uniform(-1., 1., Ngas)
gas.z = Lbox / 2 * numpy.random.uniform(-1., 1., Ngas)
else:
print 'args.grid not recognized'
print 'args.grid = ', args.grid
sys.exit(1)
# set zero velocities
gas.vx = 0. | (units.km / units.s)
gas.vy = 0. | (units.km / units.s)
gas.vz = 0. | (units.km / units.s)
# set other properties
gas.h_smooth = 0.0 * Lbox # will be set in call to hydro code
gas.u = 1 / (gamma - 1) * constants.kB * T_init / mu
gas.rho = rho_init
gas.mass = rho_init * Lbox**3 / Ngas
gas.xion = 1.2e-3
#gas.dudt=gas.u/(1.| units.Myr)
# set source in the center of the box
sources = Particles(1)
sources.x = 0.0 * Lbox
sources.y = 0.0 * Lbox
sources.z = 0.0 * Lbox
sources.luminosity = Lsrc
return gas, sources
def make_xyz(self):
from amuse.community.fi.interface import Fi
N=self.targetN
target_rms=self.target_rms
L=1| nbody_system.length
dt=0.01 | nbody_system.time
x,y,z=uniform_random_unit_cube(N).make_xyz()
vx,vy,vz=uniform_unit_sphere(N).make_xyz()
p=Particles(N)
p.x=L*x
p.y=L*y
p.z=L*z
p.h_smooth=0. * L
p.vx= 0.1*vx | (nbody_system.speed)
p.vy= 0.1*vy | (nbody_system.speed)
p.vz= 0.1*vz | (nbody_system.speed)
p.u= (0.1*0.1) | nbody_system.speed**2
p.mass=(8./N) | nbody_system.mass
sph=Fi(use_gl=False,mode='periodic',redirection='none')
sph.initialize_code()
sph.parameters.use_hydro_flag=True
sph.parameters.radiation_flag=False
sph.parameters.self_gravity_flag=False
sph.parameters.gamma=1.
sph.parameters.isothermal_flag=True
sph.parameters.integrate_entropy_flag=False
sph.parameters.timestep=dt
sph.parameters.verbosity=0
sph.parameters.periodic_box_size=2*L
sph.parameters.artificial_viscosity_alpha = 1.
sph.parameters.beta = 2.
sph.commit_parameters()
sph.gas_particles.add_particles(p)
sph.commit_particles()
# sph.start_viewer()
t=0. | nbody_system.time
rms=1.
minrms=1.
i=0
while rms > target_rms:
i+=1
t=t+(0.25 | nbody_system.time)
sph.evolve_model(t)
rho=sph.particles.rho.value_in(nbody_system.density)
rms=rho.std()/rho.mean()
minrms=min(minrms,rms)
if rms>2.*minrms or i>300:
print " RMS(rho) convergence warning:", i, rms,minrms
if i>100000:
print "i> 100k steps - not sure about this..."
print " rms:", rms
break
x=sph.particles.x.value_in(nbody_system.length)
y=sph.particles.y.value_in(nbody_system.length)
z=sph.particles.z.value_in(nbody_system.length)
del sph
return x,y,z
