def setup_sph_code(N1, N2, L, rho, u):
#rho -- local group density
#converter = nbody_system.nbody_to_si(1 | units.MSun, 1 | units.kpc)
#sph_code = sph_code(converter)#, mode = 'periodic')#, redirection = 'none')#change periodic
#sph_code.parameters.periodic_box_size = 10.0 | units.kpc
dm = Particles(N1)
dm.mass = 0.8 * (rho * L**3) / N1
#np.random.seed(12345)
dm.x = L * np.random.uniform(-0.5, 0.5, N1)
dm.y = L * np.random.uniform(-0.5, 0.5, N1)
dm.z = L * np.random.uniform(-0.5, 0.5, N1)
dm.vx = np.zeros(N1) | units.km / units.s
dm.vy = np.zeros(N1) | units.km / units.s
dm.vz = np.zeros(N1) | units.km / units.s
gas = Particles(N2)
gas.mass = 0.2 * (rho * L**3) / N2
gas.x = L * np.random.uniform(-0.5, 0.5, N2)
gas.y = L * np.random.uniform(-0.5, 0.5, N2)
gas.z = L * np.random.uniform(-0.5, 0.5, N2)
gas.vx = np.zeros(N2) | units.km / units.s
gas.vy = np.zeros(N2) | units.km / units.s
gas.vz = np.zeros(N2) | units.km / units.s
gas.u = u
gas.h_smooth = L / N2**(1 / 3.0)
dm.h_smooth = L / N1**(1 / 3.0)
#sph_code.gas_particles.add_particles(gas)
#sph_code.dm_particles.add_particles(dm)
#sph_code.commit_particles()
return gas, dm
def setup_sph_code(sph_code, N1, N2, L, rho,u):
#rho -- local group density
converter = nbody_system.nbody_to_si(1 | units.MSun, 1 | units.kpc)
sph_code = sph_code(converter, redirection = 'none')#, mode = 'periodic')#, redirection = 'none')#change periodic
#sph_code.parameters.periodic_box_size = 10.0 | units.kpc
dm = Particles(N1)
dm.mass = (rho * L**3) / N1
np.random.seed(12345)
dm.x = L * np.random.uniform(0.0, 1.0, N1)
dm.y = L * np.random.uniform(0.0, 1.0, N1)
dm.z = L * np.random.uniform(0.0, 1.0, N1)
dm.vx = np.zeros(N1) | units.km / units.s
dm.vy = np.zeros(N1) | units.km / units.s
dm.vz = np.zeros(N1) | units.km / units.s
gas = Particles(N2)
gas.mass = (rho * L**3) / N2
gas.x = L * np.random.uniform(0.0, 1.0, N2)
gas.y = L * np.random.uniform(0.0, 1.0, N2)
gas.z = L * np.random.uniform(0.0, 1.0, N2)
gas.vx = np.zeros(N2) | units.km / units.s
gas.vy = np.zeros(N2) | units.km / units.s
gas.vz = np.zeros(N2) | units.km / units.s
gas.u = u
if isinstance(sph_code, Fi):
sph_code.parameters.self_gravity_flag = True
sph_code.parameters.timestep = 5 | units.Myr
gas.h_smooth = L / N2**(1/3.0)
dm.h_smooth = L / N1**(1/3.0)
#gas.position -= 0.5 * L
sph_code.gas_particles.add_particles(gas)
sph_code.dm_particles.add_particles(dm)
sph_code.commit_particles()
return sph_code
def get_ps_from_hdf5(partfile, particle_type='all'):
""" Returns an AMUSE particle set from a FLASH
hdf5 particle file (NOT a plot file) or checkpoint file.
Keyword arguments:
partfile -- the FLASH particle file
particle_type -- the type of particle that you
want from FLASH. Can be:
star -- active FLASH particle type
sink -- sink FLASH particle type
any other string or none returns all particle types.
The default is all.
Returns:
stars -- An AMUSE particle set.
"""
import h5py
ds = h5py.File(partfile, 'r')
part_data = ds.get('tracer particles')
part_names = ds.get('particle names')
part_data = np.array(part_data)
part_names = np.array(part_names)
real_scalars = ds.get('real scalars')
part_time = real_scalars[0][1]
if (part_data.size > 1):
mass_ind = np.where(np.char.strip(part_names)=='mass')[0]
tag_ind = np.where(np.char.strip(part_names)=='tag')[0]
type_ind = np.where(np.char.strip(part_names)=='type')[0]
ct_ind = np.where(np.char.strip(part_names)=='creation_time')[0]
posx_ind = np.where(np.char.strip(part_names)=='posx')[0]
posy_ind = np.where(np.char.strip(part_names)=='posy')[0]
posz_ind = np.where(np.char.strip(part_names)=='posz')[0]
velx_ind = np.where(np.char.strip(part_names)=='velx')[0]
vely_ind = np.where(np.char.strip(part_names)=='vely')[0]
velz_ind = np.where(np.char.strip(part_names)=='velz')[0]
# Get the particle types
type_part = part_data[:,type_ind].flatten()
if (particle_type == 'star' or particle_type == 'stars'):
# Find only star particles (particle_type=1)
star_ind = np.where(type_part==1)[0]
elif (particle_type == 'sink' or particle_type == 'sinks'):
# Find only sink particles (particle_type=2)
star_ind = np.where(type_part==2)[0]
else:
star_ind = np.arange(len(type_part))
num_parts = len(star_ind)
# allocate the array
stars = Particles(num_parts)
# Masses of stars
stars.mass = part_data[star_ind,mass_ind] | u.g
# Tags of stars
stars.tag = part_data[star_ind,tag_ind]
# Creation times of stars
stars.ct = part_data[star_ind,ct_ind] | u.s
# Positions
stars.x = part_data[star_ind,posx_ind] | u.cm
stars.y = part_data[star_ind,posy_ind] | u.cm
stars.z = part_data[star_ind,posz_ind] | u.cm
# Velocities
stars.vx = part_data[star_ind,velx_ind] | u.cm/u.s
stars.vy = part_data[star_ind,vely_ind] | u.cm/u.s
stars.vz = part_data[star_ind,velz_ind] | u.cm/u.s
# Set an index attribute. Useful for some functions/codes in AMUSE.
stars.index_of_the_particle = np.arange(num_parts)
else:
print "Error: No particles found in this file!"
stars = None
return stars