def get_ps_from_yt(pltfile, particle_type="all"):
"""Take a FLASH plotfile and return an AMUSE
particle set.
Keyword arguments:
pltfile -- The FLASH hdf5 plot or checkpoint file.
Note a plotfile means there must also be
a particle file with the same ID number.
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 yt
ds = yt.load(pltfile)
dd = ds.all_data()
all_parts_mass = dd['particle_mass'].in_units('Msun')
all_parts_pos = dd['particle_position'].in_units('cm')
all_parts_vel = dd['particle_velocity'].in_units('cm/s')
if (particle_type == 'star' or particle_type == 'stars'):
# Index for only the star particles, and not including sink particles.
mass_ind = np.where(dd['particle_type'].v == 1)
elif (particle_type == 'sink' or particle_type == 'sinks'):
mass_ind = np.where(dd['particle_type'].v == 2)
else:
mass_ind = np.arange(len(all_parts_mass))
all_parts_mass = all_parts_mass[mass_ind]
all_parts_pos = all_parts_pos[mass_ind]
all_parts_vel = all_parts_vel[mass_ind]
num_parts = len(all_parts_mass.v)
stars = Particles(num_parts)
stars.mass = all_parts_mass.v | u.MSun
stars.position = all_parts_pos.v | u.cm
stars.velocity = all_parts_vel.v | u.cm/u.s
stars.index_of_the_particle = range(num_parts)
return stars
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
