def gen_scatteringIC(encounter_db, doMultipleClusters=False):
global rootDir
global cluster_name
max_number_of_rotations = 100
if doMultipleClusters:
output_ICDirectory = rootDir + '/' + cluster_name + '/Scatter_IC/'
else:
output_ICDirectory = rootDir + '/Scatter_IC/'
if not os.path.exists(output_ICDirectory): os.mkdir(output_ICDirectory)
# Set up the Kepler Workers for Subroutines Now
converter = nbody_system.nbody_to_si(1 | units.MSun, 100 | units.AU)
kepler_workers = [
Kepler(unit_converter=converter, redirection='none'),
Kepler(unit_converter=converter, redirection='none')
]
for kw in kepler_workers:
kw.initialize_code()
# Loop Through the Star_IDs
for star_ID in list(encounter_db.keys()):
output_KeyDirectory = output_ICDirectory + str(star_ID)
if not os.path.exists(output_KeyDirectory):
os.mkdir(output_KeyDirectory)
encounter_ID = 0
for encounter in encounter_db[star_ID]:
# Set Up Subdirectory for this Specific Encounter
output_EncPrefix = output_KeyDirectory + "/Enc-" + str(
encounter_ID)
# Set up Encounter Key for this Specific Encounter for this Specific Star
rotation_ID = 0
while rotation_ID <= max_number_of_rotations:
# Set Up Output Directory for this Specific Iteration
output_HDF5File = output_EncPrefix + "_Rot-" + str(
rotation_ID) + '.hdf5'
next_outFile = output_EncPrefix + "_Rot-" + str(rotation_ID +
1) + '.hdf5'
if os.path.exists(output_HDF5File):
if rotation_ID == 99:
rotation_ID += 1
continue
elif os.path.exists(next_outFile):
rotation_ID += 1
continue
# Remove Jupiter and Add Desired Planetary System
enc_bodies = replace_planetary_system(
encounter.copy(), kepler_workers=kepler_workers)
write_set_to_file(enc_bodies,
output_HDF5File,
'hdf5',
version='2.0',
close_file=True)
printID = str(star_ID) + "-" + str(encounter_ID) + "-" + str(
rotation_ID)
print(util.timestamp(),
"Finished Generating Random Encounter ID:", printID,
"...")
rotation_ID += 1
encounter_ID += 1
# Stop the Kepler Workers
for kw in kepler_workers:
kw.stop()
def update_host_star(system, converter=None, kepler_worker=None):
if kepler_worker == None:
if converter == None:
converter = nbody_system.nbody_to_si(
system.mass.sum(),
2 * np.max(system.radius.number) | system.radius.unit)
kep_p = Kepler(unit_converter=converter, redirection='none')
kep_p.initialize_code()
else:
kep_p = kepler_worker
stars = util.get_stars(system)
planets = util.get_planets(system)
p_NearestStar = planets.nearest_neighbour(stars)
for i, planet in enumerate(planets):
likely_host = p_NearestStar[i]
update_orb_elem(likely_host, [planet],
converter=converter,
kepler_worker=kep_p)
if planet.eccentricity >= 1.0:
for s in stars - likely_host:
update_orb_elem(s, [planet],
converter=converter,
kepler_worker=kep_p)
if planet.eccentricity < 1.0:
planet.host_star = s.id
break
elif planet.eccentricity >= 1.0:
planet.host_star = -1
else:
planet.host_star = likely_host.id
if kepler_worker == None:
kep_p.stop()
def integrate_system(N, t_end, seed=None):
total_mass = N | units.MSun
length = 1 | units.parsec
converter = nbody_system.nbody_to_si(total_mass, length)
gravity = ph4(convert_nbody=converter)
gravity.initialize_code()
gravity.parameters.set_defaults()
gravity.parameters.epsilon_squared = (0.0 | units.parsec)**2
if seed is not None: numpy.random.seed(seed)
stars = new_plummer_model(N, convert_nbody=converter)
stars.mass = total_mass / N
stars.scale_to_standard(
convert_nbody=converter,
smoothing_length_squared=gravity.parameters.epsilon_squared)
id = numpy.arange(N)
stars.id = id + 1
stars.radius = 0.5 / N | units.parsec
gravity.particles.add_particles(stars)
stopping_condition = gravity.stopping_conditions.collision_detection
stopping_condition.enable()
init_smalln(converter)
kep = Kepler(unit_converter=converter)
kep.initialize_code()
multiples_code = multiples.Multiples(gravity, new_smalln, kep, constants.G)
multiples_code.neighbor_perturbation_limit = 0.05
multiples_code.global_debug = 1
###BOOKLISTSTOP2###
# global_debug = 0: no output from multiples
# 1: minimal output
# 2: debugging output
# 3: even more output
print('')
print('multiples_code.neighbor_veto =', \
multiples_code.neighbor_veto)
print('multiples_code.neighbor_perturbation_limit =', \
multiples_code.neighbor_perturbation_limit)
print('multiples_code.retain_binary_apocenter =', \
multiples_code.retain_binary_apocenter)
print('multiples_code.wide_perturbation_limit =', \
multiples_code.wide_perturbation_limit)
time = numpy.sqrt(length**3 / (constants.G * total_mass))
print('\ntime unit =', time.in_(units.Myr))
###BOOKLISTSTART3###
E0 = print_diagnostics(multiples_code)
multiples_code.evolve_model(t_end)
print_diagnostics(multiples_code, E0)
###BOOKLISTSTOP3###
gravity.stop()
kep.stop()
stop_smalln()
def integrate_system(N, t_end, seed=None):
gravity = ph4()
gravity.initialize_code()
gravity.parameters.set_defaults()
if seed is not None: numpy.random.seed(seed)
stars = new_plummer_model(N)
stars.mass = 1./N | nbody_system.mass
stars.scale_to_standard(smoothing_length_squared
= gravity.parameters.epsilon_squared)
id = numpy.arange(N)
stars.id = id+1
# Set dynamical radii for encounters.
stars.radius = 0.5*stars.mass.number | nbody_system.length
gravity.particles.add_particles(stars)
stopping_condition = gravity.stopping_conditions.collision_detection
stopping_condition.enable()
init_smalln()
kep = Kepler(unit_converter=None)
kep.initialize_code()
multiples_code = multiples.Multiples(gravity, new_smalln, kep)
multiples_code.neighbor_perturbation_limit = 0.05
multiples_code.global_debug = 1
# global_debug = 0: no output from multiples
# 1: minimal output
# 2: debugging output
# 3: even more output
print('')
print('multiples_code.neighbor_veto =', \
multiples_code.neighbor_veto)
print('multiples_code.neighbor_perturbation_limit =', \
multiples_code.neighbor_perturbation_limit)
print('multiples_code.retain_binary_apocenter =', \
multiples_code.retain_binary_apocenter)
print('multiples_code.wide_perturbation_limit =', \
multiples_code.wide_perturbation_limit)
# Advance the system.
E0 = print_diagnostics(multiples_code)
multiples_code.evolve_model(t_end)
print_diagnostics(multiples_code, E0)
gravity.stop()
kep.stop()
stop_smalln()
def init_kepler(star1, star2):
try:
star1.mass.value_in(units.kg) # see if SI units, throw exception if not
unit_converter \
= nbody_system.nbody_to_si(star1.mass + star2.mass,
(star2.position-star1.position).length())
except Exception as ex:
unit_converter = None
kep = Kepler(unit_converter, redirection = "none")
kep.initialize_code()
return kep
def new_system(star_mass=1 | units.MSun,
star_radius=1 | units.RSun,
disk_minimum_radius=0.05 | units.AU,
disk_maximum_radius=10 | units.AU,
disk_mass=20 | MEarth,
accurancy=0.0001,
planet_density=3 | units.g / units.cm**3,
rng=None,
kepler=None):
central_particle = Particle()
central_particle.mass = star_mass
central_particle.position = (0, 0, 0) | units.AU
central_particle.velocity = (0, 0, 0) | units.kms
central_particle.radius = star_radius
central_particle.name = "star"
central_particle.type = "star"
central_particle.id = 0
if rng is None:
rng = numpy.random
converter = nbody_system.nbody_to_si(1 | units.MSun, 1 | units.AU)
if kepler is None:
kepler = Kepler(converter)
kepler.initialize_code()
m, r, f = new_planet_distribution(disk_minimum_radius, disk_maximum_radius,
disk_mass, accurancy)
planets = make_planets(central_particle,
m,
r,
density=planet_density,
phi=0,
theta=None,
kepler=kepler,
rng=rng)
planets.name = "planet"
planets.type = "planet"
for i in range(len(planets)):
planets[i].id = i
central_particle.planets = planets
kepler.stop()
p = Particles()
p.add_particle(central_particle)
return p
def get_component_binary_elements(comp1, comp2):
kep = Kepler(redirection="none")
kep.initialize_code()
mass = comp1.mass + comp2.mass
pos = comp2.position - comp1.position
vel = comp2.velocity - comp1.velocity
kep.initialize_from_dyn(mass, pos[0], pos[1], pos[2], vel[0], vel[1],
vel[2])
a, e = kep.get_elements()
r = kep.get_separation()
E, J = kep.get_integrals() # per unit reduced mass, note
kep.stop()
return mass, a, e, r, E
def get_binary_elements(p):
comp1 = p.child1
comp2 = p.child2
kep = Kepler(redirection="none")
kep.initialize_code()
mass = comp1.mass + comp2.mass
pos = [comp2.x - comp1.x, comp2.y - comp1.y, comp2.z - comp1.z]
vel = [comp2.vx - comp1.vx, comp2.vy - comp1.vy, comp2.vz - comp1.vz]
kep.initialize_from_dyn(mass, pos[0], pos[1], pos[2], vel[0], vel[1],
vel[2])
a, e = kep.get_elements()
kep.stop()
return mass, a, e
def relative_position_and_velocity_from_orbital_elements(
mass1, mass2, semimajor_axis, eccentricity, mean_anomaly, seed=None):
"""
Function that returns relative positions and velocity vectors or orbiters with masses
mass2 of the central body with mass mass1 in Cartesian coordinates;
for vectors of orbital elements -- semi-major axes, eccentricities, mean anomalies.
3D orientation of orbits (inclination, longitude of ascending node and argument of periapsis) are random.
(cos(incl) is uniform -1--1, longitude of ascending node and argument of periapsis are uniform 0--2pi)
Assuming mass1 is static in the center [0,0,0] m, [0,0,0] km/s (that is mass2<<mass1)
"""
position_vectors = []
velocity_vectors = []
converter = nbody_system.nbody_to_si(1 | units.MSun, 1 | units.AU)
kepler = Kepler(converter)
kepler.initialize_code()
r_vec = (0., 0., 0.) | units.AU
v_vec = (0., 0., 0.) | units.kms
# to change seed for each particle
if seed is not None:
i = 0
for m2_i, a_i, ecc_i, ma_i in zip(mass2, semimajor_axis, eccentricity,
mean_anomaly):
#print m2_i, a_i, ecc_i, ma_i
if seed is not None:
kepler.set_random(seed + i)
i = i + 1
kepler.initialize_from_elements(mass=(mass1 + m2_i),
semi=a_i,
ecc=ecc_i,
mean_anomaly=ma_i,
random_orientation=-1)
ri = kepler.get_separation_vector()
vi = kepler.get_velocity_vector()
# this is to get ~half of the orbits retrograde (that is with inclination
# of 90--180 degrees) --> velocity = -velocity
vel_vec_dir = numpy.random.random()
if (vel_vec_dir <= 0.5):
vel_orientation = 1.
else:
vel_orientation = -1.
position_vectors.append([ri[0], ri[1], ri[2]])
velocity_vectors.append([
vel_orientation * vi[0], vel_orientation * vi[1],
vel_orientation * vi[2]
])
kepler.stop()
return position_vectors, velocity_vectors
def run_kepler(mass, semi, ecc, time):
kep = Kepler(redirection='none')
kep.initialize_code()
kep.set_longitudinal_unit_vector(1.0, 1.0,
0.0)
kep.initialize_from_elements(mass, semi, ecc)
a,e = kep.get_elements()
p = kep.get_periastron()
print "elements:", a, e, p
kep.transform_to_time(time)
x,y,z = kep.get_separation_vector()
print "separation:", x,y,z
x,y,z = kep.get_longitudinal_unit_vector()
print "longitudinal:", x,y,z
pos = [1, 0, 0] | nbody_system.length
vel = [0, 0.5, 0] | nbody_system.speed
kep.initialize_from_dyn(mass, pos[0], pos[1], pos[2],
vel[0], vel[1], vel[2])
a,e = kep.get_elements()
p = kep.get_periastron()
print "elements:", a, e, p
kep.transform_to_time(time)
x,y,z = kep.get_separation_vector()
print "separation:", x,y,z
x,y,z = kep.get_velocity_vector()
print "velocity:", x,y,z
x,y,z = kep.get_longitudinal_unit_vector()
print "longitudinal:", x,y,z
kep.set_random(42)
kep.make_binary_scattering(0.5 | nbody_system.mass,
0.5,
0.5 | nbody_system.mass,
0.0 | nbody_system.speed,
0.0 | nbody_system.length,
1.e-6,
0)
kep.stop()
def new_multiples_code(gravity, converter):
"""
Initialise a multiples instance with specified gravity code.
The gravity code must support stopping conditions (collision detection).
"""
gravity.parameters.epsilon_squared = (0.0 | units.parsec)**2
stopping_condition = gravity.stopping_conditions.collision_detection
stopping_condition.enable()
init_smalln(converter)
kep = Kepler(unit_converter=converter)
kep.initialize_code()
multiples_code = multiples.Multiples(
gravity,
new_smalln,
kep,
constants.G,
)
multiples_code.neighbor_perturbation_limit = 0.05
multiples_code.global_debug = 0
return multiples_code
def orbital_parameters_for_the_planets(bodies, verbose=True):
from amuse.community.kepler.interface import Kepler
kepler = Kepler(redirection = "none")
kepler.initialize_code()
# kep_converter=nbody_system.nbody_to_si(1|units.MSun, 10|units.AU)
converter=nbody_system.nbody_to_si(1.0|units.MSun, 1|units.AU)
a = [] | units.AU
e = []
m = [] | units.MSun
name = []
for bi in bodies[1:]:
ai, ei, M, ms = calculate_orbital_elements(bodies[0], bi, kepler, converter)
name.append(bi.name)
a.append(ai)
e.append(ei)
m.append(ms)
kepler.stop()
if verbose:
for i in range(len(a)):
print("Planet: ", name[i], a[i], e[i], m[i])
return a, e
def update_orb_elem(host_star, planets, converter=None, kepler_worker=None):
if kepler_worker == None:
if converter == None:
tot_sys = Particles(particles=(host_star, planets))
converter = nbody_system.nbody_to_si(tot_sys.mass.sum(),
2 * host_star.radius)
kep_p = Kepler(unit_converter=converter, redirection='none')
kep_p.initialize_code()
else:
kep_p = kepler_worker
for planet in planets:
total_mass = host_star.mass + planet.mass
kep_pos = host_star.position - planet.position
kep_vel = host_star.velocity - planet.velocity
kep_p.initialize_from_dyn(total_mass, kep_pos[0], kep_pos[1],
kep_pos[2], kep_vel[0], kep_vel[1],
kep_vel[2])
planet.semimajor_axis, planet.eccentricity = kep_p.get_elements()
planet.period = kep_p.get_period()
planet.true_anomaly, planet.mean_anomaly = kep_p.get_angles()
if kepler_worker == None:
kep_p.stop()
def new_kepler_si(self):
unit_converter = nbody_system.nbody_to_si(1 | units.MSun, 1 | units.AU)
kepler = Kepler(unit_converter)
kepler.initialize_code()
return kepler
def test11(self):
"""
testing orbital_elements_for_rel_posvel_arrays for unbound orbits
"""
from amuse.community.kepler.interface import Kepler
numpy.random.seed(66)
N = 10
mass_sun = 1. | units.MSun
mass1 = numpy.ones(N) * mass_sun
mass2 = numpy.zeros(N) | units.MSun
semi_major_axis=-1000.*(random.random(N)) | units.AU
eccentricity = (1.+random.random(N))*10.-9.
inclination = numpy.pi*random.random(N)
longitude_of_the_ascending_node = 2.*numpy.pi*random.random(N)-numpy.pi
argument_of_periapsis = 2.*numpy.pi*random.random(N)-numpy.pi
# kepler.initialize_from_elements initializes orbits with mean_anomaly=0 and true_anomaly=0
true_anomaly = 0.*(360.*random.random(N)-180.)
comets = datamodel.Particles(N)
converter = nbody_system.nbody_to_si(1|units.MSun,1|units.AU)
kepler = Kepler(converter)
kepler.initialize_code()
for i,arg in enumerate(zip(mass1,mass2,semi_major_axis,eccentricity,true_anomaly,inclination,
longitude_of_the_ascending_node,argument_of_periapsis)):
kepler.initialize_from_elements(mass=(mass1[i]+mass2[i]),
semi=semi_major_axis[i],
ecc=eccentricity[i])
ri = kepler.get_separation_vector()
vi = kepler.get_velocity_vector()
om = longitude_of_the_ascending_node[i]
w = argument_of_periapsis[i]
incl = inclination[i]
a1 = ([numpy.cos(om), -numpy.sin(om), 0.0], [numpy.sin(om), numpy.cos(om), 0.0], [0.0, 0.0, 1.0])
a2 = ([1.0, 0.0, 0.0], [0.0, numpy.cos(incl), -numpy.sin(incl)], [0.0, numpy.sin(incl), numpy.cos(incl)])
a3 = ([numpy.cos(w), -numpy.sin(w), 0.0], [numpy.sin(w), numpy.cos(w), 0.0], [0.0, 0.0, 1.0])
A = numpy.dot(numpy.dot(a1,a2),a3)
r_vec = numpy.dot(A,numpy.reshape(ri,3,1))
v_vec = numpy.dot(A,numpy.reshape(vi,3,1))
r = (0.0, 0.0, 0.0) | units.AU
v = (0.0, 0.0, 0.0) | (units.AU / units.day)
r[0] = r_vec[0]
r[1] = r_vec[1]
r[2] = r_vec[2]
v[0] = v_vec[0]
v[1] = v_vec[1]
v[2] = v_vec[2]
comets[i].mass = mass2[i]
comets[i].position = r_vec
comets[i].velocity = v_vec
kepler.stop()
semi_major_axis_ext, eccentricity_ext, ta_ext, inclination_ext, \
longitude_of_the_ascending_node_ext, argument_of_periapsis_ext = \
orbital_elements(comets.position,
comets.velocity,
comets.mass + mass_sun,
G=constants.G)
self.assertAlmostEqual(semi_major_axis,semi_major_axis_ext.in_(units.AU))
self.assertAlmostEqual(eccentricity,eccentricity_ext)
self.assertAlmostEqual(inclination,inclination_ext)
self.assertAlmostEqual(longitude_of_the_ascending_node,longitude_of_the_ascending_node_ext)
self.assertAlmostEqual(argument_of_periapsis,argument_of_periapsis_ext)
self.assertAlmostEqual(true_anomaly,ta_ext)
gravity.parameters.gpu_id = gpu_ID # Setting Up the Stopping Conditions in PH4 stopping_condition = gravity.stopping_conditions.collision_detection stopping_condition.enable() sys.stdout.flush() # Adding and Committing Particles to PH4 gravity.particles.add_particles(MasterSet) gravity.commit_particles() # Starting the AMUSE Channel for PH4 grav_channel = gravity.particles.new_channel_to(MasterSet) # Initializing Kepler and SmallN kep = Kepler(None, redirection="none") kep.initialize_code() util.init_smalln() # Initializing MULTIPLES multiples_code = multiples.Multiples(gravity, util.new_smalln, kep) multiples_code.neighbor_distance_factor = 1.0 multiples_code.neighbor_veto = True multiples_code.evolve_model(time) gravity.synchronize_model() # Copy values from the module to the set in memory. grav_channel.copy() # Copy the index (ID) as used in the module to the id field in # memory. The index is not copied by default, as different
def start_kepler(self, mass_unit, length_unit):
unit_converter = nbody_system.nbody_to_si(mass_unit, length_unit)
self.kepler = Kepler(unit_converter,
redirection="none" if self.debug else "null")
self.kepler.initialize_code()
#-----------------------------------------------------------------
assert is_mpd_running()
# Instantiate workers once only and pass to scatter3 as arguments.
gravity = SmallN(redirection="none")
#gravity = SmallN(redirection = "none", debugger="valgrind") # search for
# memory leaks
gravity.initialize_code()
gravity.parameters.set_defaults()
gravity.parameters.timestep_parameter = accuracy_parameter
gravity.parameters.unperturbed_threshold = gamma
kep = Kepler(redirection="none") #, debugger="gdb")
kep.initialize_code()
kep.set_random(random_seed) # ** Note potential conflict between C++
# ** and Python random generators.
# Timing:
cpu = numpy.zeros(4)
for i in range(nscatter):
final, dcpu = scatter3(init, kep, gravity, gamma, delta_t, t_end)
cpu += dcpu
print ''
if final.is_over == 0:
def new_kepler():
from amuse.community.kepler.interface import Kepler
converter = nbody_system.nbody_to_si(1 | units.MSun, 1 | units.AU)
kepler = Kepler(converter)
kepler.initialize_code()
return kepler
def run_ph4(options,
time=None,
stars=None,
mc_root_to_tree=None,
randomize=True):
infile = options.infile
outfile = options.outfile
restart_file = options.restart_file
number_of_stars = options.N
number_of_binaries = options.Nbin
end_time = options.t_end | nbody_system.time
delta_t = options.delta_t | nbody_system.time
n_workers = options.n_workers
use_gpu = options.use_gpu
gpu_worker = options.gpu_worker
salpeter = options.salpeter
accuracy_parameter = options.accuracy_parameter
softening_length = options.softening_length | nbody_system.length
manage_encounters = options.manage_encounters
random_seed = options.random_seed
if randomize:
if random_seed <= 0:
numpy.random.seed()
random_seed = numpy.random.randint(1, pow(2, 31) - 1)
numpy.random.seed(random_seed)
print "random seed =", random_seed
if infile is not None: print "input file =", infile
if restart_file is not None: print "restart file =", restart_file
if restart_file is not None and infile is not None:
print "restart file overrides input file"
print "end_time =", end_time.number
print "delta_t =", delta_t.number
print "n_workers =", n_workers
print "use_gpu =", use_gpu
print "manage_encounters =", manage_encounters
print "n =", number_of_stars
print "nbin=", number_of_binaries
print "\ninitializing the gravity module"
sys.stdout.flush()
init_smalln()
# Note that there are actually three GPU options:
#
# 1. use the GPU code and allow GPU use (default)
# 2. use the GPU code but disable GPU use (-g)
# 3. use the non-GPU code (-G)
if gpu_worker == 1:
try:
#gravity = GravityModule(number_of_workers = n_workers,
# redirection = "xterm")
gravity = GravityModule(number_of_workers=n_workers,
redirection="none",
mode="gpu")
except Exception as ex:
gravity = GravityModule(number_of_workers=n_workers,
redirection="none")
else:
gravity = GravityModule(number_of_workers=n_workers,
redirection="none")
gravity.initialize_code()
gravity.parameters.set_defaults()
if softening_length < 0.0 | nbody_system.length:
# Use ~interparticle spacing. Assuming standard units here. TODO
eps2 = 0.25*(float(number_of_stars))**(-0.666667) \
| nbody_system.length**2
else:
eps2 = softening_length * softening_length
print 'softening length =', eps2.sqrt()
gravity.parameters.timestep_parameter = accuracy_parameter
gravity.parameters.epsilon_squared = eps2
gravity.parameters.use_gpu = use_gpu
kep = Kepler(redirection="none")
kep.initialize_code()
multiples_code = None
Xtra = numpy.zeros(2)
#-----------------------------------------------------------------
if (restart_file is None
or not os.path.exists(restart_file + ".stars.hdf5")
) and infile is None and stars is None:
print "making a Plummer model"
stars = new_plummer_model(number_of_stars)
id = numpy.arange(number_of_stars)
stars.id = id + 1
print "setting particle masses and radii"
if salpeter == 0:
print 'equal masses'
total_mass = 1.0 | nbody_system.mass
scaled_mass = total_mass / number_of_stars
else:
print 'salpeter mass function'
scaled_mass = new_salpeter_mass_distribution_nbody(number_of_stars)
stars.mass = scaled_mass
print "centering stars"
stars.move_to_center()
print "scaling stars to virial equilibrium"
stars.scale_to_standard(
smoothing_length_squared=gravity.parameters.epsilon_squared)
time = 0.0 | nbody_system.time
total_mass = stars.mass.sum()
ke = pa.kinetic_energy(stars)
kT = ke / (1.5 * number_of_stars)
# Set dynamical radii (assuming virial equilibrium and standard
# units). Note that this choice should be refined, and updated
# as the system evolves. Probably the choice of radius should be
# made entirely in the multiples module. TODO. In these units,
# M = 1 and <v^2> = 0.5, so the mean 90-degree turnaround impact
# parameter is
#
# b_90 = G (m_1+m_2) / vrel^2
# = 2 <m> / 2<v^2>
# = 2 / N for equal masses
#
# Taking r_i = m_i / 2<v^2> = m_i in virial equilibrium means
# that, approximately, "contact" means a 90-degree deflection (r_1
# + r_2 = b_90). A more conservative choice with r_i less than
# this value will isolates encounters better, but also place more
# load on the large-N dynamical module.
stars.radius = stars.mass.number | nbody_system.length
if number_of_binaries > 0:
# Turn selected stars into binary components.
# Only tested for equal-mass case.
added_mass = 0.0 | nbody_system.mass
# Work with energies rather than semimajor axes.
Emin = 10 * kT
Emax = 20 * kT
ecc = 0.1
id_count = number_of_stars
nbin = 0
for i in range(0, number_of_stars,
number_of_stars / number_of_binaries):
# Star i is CM, becomes component, add other star at end.
nbin += 1
mass = stars[i].mass
#new_mass = numpy.random.uniform()*mass # uniform q?
new_mass = mass # uniform q?
mbin = mass + new_mass
fac = new_mass / mbin
E = Emin + numpy.random.uniform() * (Emax - Emin)
a = 0.5 * nbody_system.G * mass * new_mass / E
kep.initialize_from_elements(mbin, a, ecc)
dr = quantities.AdaptingVectorQuantity()
dr.extend(kep.get_separation_vector())
dv = quantities.AdaptingVectorQuantity()
dv.extend(kep.get_velocity_vector())
newstar = datamodel.Particles(1)
newstar.mass = new_mass
newstar.position = stars[i].position + (1 - fac) * dr
newstar.velocity = stars[i].velocity + (1 - fac) * dv
newstar.radius = newstar.mass.number | nbody_system.length
#newstar.radius = 3.0*stars[i].radius # HACK: try to force collision
# stars[i].mass = mass
stars[i].position = stars[i].position - fac * dr
stars[i].velocity = stars[i].velocity - fac * dv
id_count += 1
newstar.id = id_count
stars.add_particles(newstar)
added_mass += new_mass
if nbin >= number_of_binaries: break
kep.stop()
print 'created', nbin, 'binaries'
sys.stdout.flush()
stars.mass = stars.mass * total_mass / (total_mass + added_mass)
number_of_stars += nbin
Xtra = numpy.zeros(2)
print "recentering stars"
stars.move_to_center()
sys.stdout.flush()
stars.savepoint(time)
print ''
print "adding particles"
# print stars
sys.stdout.flush()
gravity.particles.add_particles(stars)
gravity.commit_particles()
else:
print "Restart detected. Loading parameters from restart."
new_end = options.t_end
stars, time, multiples_code, Xtra = MRest.read_state_from_file(
restart_file, gravity, new_smalln, kep)
options.t_end = new_end
total_mass = stars.mass.sum()
ke = pa.kinetic_energy(stars)
kT = ke / (1.5 * number_of_stars)
# print "IDs:", stars.id.number
print ''
print "number_of_stars =", number_of_stars
print "evolving to time =", end_time.number, \
"in steps of", delta_t.number
sys.stdout.flush()
# Channel to copy values from the code to the set in memory.
channel = gravity.particles.new_channel_to(stars)
stopping_condition = gravity.stopping_conditions.collision_detection
stopping_condition.enable()
# -----------------------------------------------------------------
# Create the coupled code and integrate the system to the desired
# time, managing interactions internally.
kep = init_kepler(stars[0], stars[1])
if not multiples_code:
multiples_code = multiples.Multiples(gravity, new_smalln, kep)
multiples_code.neighbor_distance_factor = 1.0
multiples_code.neighbor_veto = True
#multiples_code.neighbor_distance_factor = 2.0
#multiples_code.neighbor_veto = True
multiples_code.retain_binary_apocenter = False
print ''
print 'multiples_code.initial_scale_factor =', \
multiples_code.initial_scale_factor
print 'multiples_code.neighbor_distance_factor =', \
multiples_code.neighbor_distance_factor
print 'multiples_code.neighbor_veto =', \
multiples_code.neighbor_veto
print 'multiples_code.final_scale_factor =', \
multiples_code.final_scale_factor
print 'multiples_code.initial_scatter_factor =', \
multiples_code.initial_scatter_factor
print 'multiples_code.final_scatter_factor =', \
multiples_code.final_scatter_factor
print 'multiples_code.retain_binary_apocenter =', \
multiples_code.retain_binary_apocenter
# if mc_root_to_tree is not None:
# multiples_code.root_to_tree = mc_root_to_tree
# print 'multiples code re-loaded with binary trees snapshot'
pre = "%%% "
E0, cpu0 = print_log(pre, time, multiples_code)
while time < end_time:
time += delta_t
multiples_code.evolve_model(time)
# Copy values from the module to the set in memory.
channel.copy()
# Copy the index (ID) as used in the module to the id field in
# memory. The index is not copied by default, as different
# codes may have different indices for the same particle and
# we don't want to overwrite silently.
channel.copy_attribute("index_in_code", "id")
print_log(pre, time, multiples_code, E0, cpu0)
stars.savepoint(time)
MRest.write_state_to_file(time,
stars,
gravity,
multiples_code,
options.restart_file,
Xtra,
backup=1)
sys.stdout.flush()
#-----------------------------------------------------------------
if not outfile is None:
# Write data to a file.
f = open(outfile, 'w')
#--------------------------------------------------
# Need to save top-level stellar data and parameters.
# Need to save multiple data and parameters.
f.write('%.15g\n' % time.number)
for s in multiples_code.stars:
write_star(s, f)
#--------------------------------------------------
f.close()
print 'wrote file', outfile
print ''
gravity.stop()
def compress_binary_components(comp1, comp2, scale):
# Compress the two-body system consisting of comp1 and comp2 to
# lie within distance scale of one another.
pos1 = comp1.position
pos2 = comp2.position
sep12 = ((pos2 - pos1)**2).sum()
if sep12 > scale * scale:
print('\ncompressing components', int(comp1.id.number), \
'and', int(comp2.id.number), 'to separation', scale.number)
sys.stdout.flush()
mass1 = comp1.mass
mass2 = comp2.mass
total_mass = mass1 + mass2
vel1 = comp1.velocity
vel2 = comp2.velocity
cmpos = (mass1 * pos1 + mass2 * pos2) / total_mass
cmvel = (mass1 * vel1 + mass2 * vel2) / total_mass
# For now, create and delete a temporary kepler
# process to handle the transformation. Obviously
# more efficient to define a single kepler at the
# start of the calculation and reuse it.
kep = Kepler(redirection="none")
kep.initialize_code()
mass = comp1.mass + comp2.mass
rel_pos = pos2 - pos1
rel_vel = vel2 - vel1
kep.initialize_from_dyn(mass, rel_pos[0], rel_pos[1], rel_pos[2],
rel_vel[0], rel_vel[1], rel_vel[2])
M, th = kep.get_angles()
a, e = kep.get_elements()
if e < 1:
peri = a * (1 - e)
apo = a * (1 + e)
else:
peri = a * (e - 1)
apo = 2 * a # OK - used ony to reset scale
limit = peri + 0.01 * (apo - peri)
if scale < limit: scale = limit
if M < 0:
# print 'approaching'
kep.advance_to_periastron()
kep.advance_to_radius(limit)
else:
# print 'receding'
if kep.get_separation() < scale:
kep.advance_to_radius(limit)
else:
kep.return_to_radius(scale)
# a,e = kep.get_elements()
# r = kep.get_separation()
# E,J = kep.get_integrals()
# print 'kepler: a,e,r =', a.number, e.number, r.number
# print 'E, J =', E, J
# Note: if periastron > scale, we are now just past periastron.
new_rel_pos = kep.get_separation_vector()
new_rel_vel = kep.get_velocity_vector()
kep.stop()
# Enew = 0
# r2 = 0
# for k in range(3):
# Enew += 0.5*(new_rel_vel[k].number)**2
# r2 += (new_rel_pos[k].number)**2
# rnew = math.sqrt(r2)
# Enew -= mass.number/r1
# print 'E, Enew, rnew =', E.number, E1, r1
# Problem: the vectors returned by kepler are lists,
# not numpy arrays, and it looks as though we can say
# comp1.position = pos, but not comp1.position[k] =
# xxx, as we'd like... Also, we don't know how to
# copy a numpy array with units... TODO
newpos1 = pos1 - pos1 # stupid trick to create zero vectors
newpos2 = pos2 - pos2 # with the proper form and units...
newvel1 = vel1 - vel1
newvel2 = vel2 - vel2
frac2 = mass2 / total_mass
for k in range(3):
dxk = new_rel_pos[k]
dvk = new_rel_vel[k]
newpos1[k] = cmpos[k] - frac2 * dxk
newpos2[k] = cmpos[k] + (1 - frac2) * dxk
newvel1[k] = cmvel[k] - frac2 * dvk
newvel2[k] = cmvel[k] + (1 - frac2) * dvk
# Perform the changes to comp1 and comp2, and recursively
# transmit them to the (currently absolute) coordinates of
# all lower components.
offset_particle_tree(comp1, newpos1 - pos1, newvel1 - vel1)
offset_particle_tree(comp2, newpos2 - pos2, newvel2 - vel2)
def run_ph4(infile=None,
number_of_stars=40,
end_time=10 | nbody_system.time,
delta_t=1 | nbody_system.time,
n_workers=1,
use_gpu=1,
gpu_worker=1,
accuracy_parameter=0.1,
softening_length=-1 | nbody_system.length,
manage_encounters=1,
random_seed=1234):
if random_seed <= 0:
numpy.random.seed()
random_seed = numpy.random.randint(1, pow(2, 31) - 1)
numpy.random.seed(random_seed)
print("random seed =", random_seed)
if infile != None: print("input file =", infile)
print("end_time =", end_time.number)
print("delta_t =", delta_t.number)
print("n_workers =", n_workers)
print("use_gpu =", use_gpu)
print("manage_encounters =", manage_encounters)
print("\ninitializing the gravity module")
sys.stdout.flush()
# Note that there are actually three GPU options to test:
#
# 1. use the GPU code and allow GPU use (default)
# 2. use the GPU code but disable GPU use (-g)
# 3. use the non-GPU code (-G)
if gpu_worker == 1:
try:
gravity = grav(number_of_workers=n_workers,
redirection="none",
mode="gpu")
except Exception as ex:
gravity = grav(number_of_workers=n_workers, redirection="none")
else:
gravity = grav(number_of_workers=n_workers, redirection="none")
gravity.initialize_code()
gravity.parameters.set_defaults()
#-----------------------------------------------------------------
if infile == None:
print("making a Plummer model")
stars = new_plummer_model(number_of_stars)
id = numpy.arange(number_of_stars)
stars.id = id + 1
print("setting particle masses and radii")
#stars.mass = (1.0 / number_of_stars) | nbody_system.mass
scaled_mass = new_salpeter_mass_distribution_nbody(number_of_stars)
stars.mass = scaled_mass
stars.radius = 0.02 | nbody_system.length
print("centering stars")
stars.move_to_center()
print("scaling stars to virial equilibrium")
stars.scale_to_standard(
smoothing_length_squared=gravity.parameters.epsilon_squared)
time = 0.0 | nbody_system.time
sys.stdout.flush()
else:
# Read the input data. Units are dynamical.
print("reading file", infile)
id = []
mass = []
pos = []
vel = []
f = open(infile, 'r')
count = 0
for line in f:
if len(line) > 0:
count += 1
cols = line.split()
if count == 1: snap = int(cols[0])
elif count == 2: number_of_stars = int(cols[0])
elif count == 3: time = float(cols[0]) | nbody_system.time
else:
if len(cols) >= 8:
id.append(int(cols[0]))
mass.append(float(cols[1]))
pos.append(
(float(cols[2]), float(cols[3]), float(cols[4])))
vel.append(
(float(cols[5]), float(cols[6]), float(cols[7])))
f.close()
stars = datamodel.Particles(number_of_stars)
stars.id = id
stars.mass = mass | nbody_system.mass
stars.position = pos | nbody_system.length
stars.velocity = vel | nbody_system.speed
stars.radius = 0. | nbody_system.length
# print "IDs:", stars.id.number
sys.stdout.flush()
#-----------------------------------------------------------------
if softening_length == -1 | nbody_system.length:
eps2 = 0.25*(float(number_of_stars))**(-0.666667) \
| nbody_system.length**2
else:
eps2 = softening_length * softening_length
gravity.parameters.timestep_parameter = accuracy_parameter
gravity.parameters.epsilon_squared = eps2
gravity.parameters.use_gpu = use_gpu
# gravity.parameters.manage_encounters = manage_encounters
print("adding particles")
# print stars
sys.stdout.flush()
gravity.particles.add_particles(stars)
gravity.commit_particles()
print('')
print("number_of_stars =", number_of_stars)
print("evolving to time =", end_time.number, \
"in steps of", delta_t.number)
sys.stdout.flush()
E0 = print_log(time, gravity)
# Channel to copy values from the code to the set in memory.
channel = gravity.particles.new_channel_to(stars)
stopping_condition = gravity.stopping_conditions.collision_detection
stopping_condition.enable()
kep = Kepler(redirection="none")
kep.initialize_code()
multiples_code = multiples.Multiples(gravity, new_smalln, kep)
while time < end_time:
time += delta_t
multiples_code.evolve_model(time)
# Copy values from the module to the set in memory.
channel.copy()
# Copy the index (ID) as used in the module to the id field in
# memory. The index is not copied by default, as different
# codes may have different indices for the same particle and
# we don't want to overwrite silently.
channel.copy_attribute("index_in_code", "id")
print_log(time, gravity, E0)
sys.stdout.flush()
print('')
gravity.stop()
else:
directory = os.getcwd()
cluster_name = directory.split("/")[-1]
base_planet_ID = 50000
orig_stdout = sys.stdout
log_file = open(os.getcwd() + "/cut_encounters.log", "w")
sys.stdout = log_file
# Create the Kepler Workers
KeplerWorkerList = []
converter = nbody_system.nbody_to_si(1 | units.MSun, 100 | units.AU)
for i in range(3):
KeplerWorkerList.append(
Kepler(unit_converter=converter, redirection='none'))
KeplerWorkerList[-1].initialize_code()
# Read in Encounter Directory
encounter_file = open(os.getcwd() + "/" + cluster_name + "_encounters.pkl",
"rb")
encounter_db = pickle.load(encounter_file)
encounter_file.close()
sys.stdout.flush()
print(util.timestamp(), "Performing First Cut on Encounter Database ...")
print(len(encounter_db.keys()))
sys.stdout.flush()
# Perform a Cut on the Encounter Database
for star_ID in list(encounter_db.keys()):
# Cut Out Stars Recorded with Only Initialization Pickups
def CutOrAdvance(enc_bodies, primary_sysID, converter=None, **kwargs):
bodies = enc_bodies.copy()
KeplerWorkerList = kwargs.get("kepler_workers", None)
# Initialize Kepler Workers if they Don't Exist
if KeplerWorkerList == None:
if converter == None:
converter = nbody_system.nbody_to_si(
bodies.mass.sum(),
2 * np.max(bodies.radius.number) | bodies.radius.unit)
KeplerWorkerList = []
for i in range(3):
KeplerWorkerList.append(
Kepler(unit_converter=converter, redirection='none'))
KeplerWorkerList[-1].initialize_code()
systems = stellar_systems.get_heirarchical_systems_from_set(bodies, \
kepler_workers=KeplerWorkerList[:2], \
RelativePosition=False)
# Deal with Possible Key Issues with Encounters with 3+ Star Particles Being Run More than Other Systems ...
if int(primary_sysID) not in list(systems.keys()):
print(
"...: Error: Previously run binary system has been found! Not running this system ..."
)
print(primary_sysID)
print(list(systems.keys()))
print("---------------------------------")
return None
# As this function is pulling from Multiples, there should never be more or less than 2 "Root" Particles ...
if len(systems) != 2:
print(
"...: Error: Encounter has more roots than expected! Total Root Particles:",
len(systems))
print(bodies)
print("---------------------------------")
return None
# Assign the Primary System to #1 and Perturbing System to #2
sys_1 = systems[int(primary_sysID)]
secondary_sysID = [
key for key in list(systems.keys()) if key != int(primary_sysID)
][0]
sys_2 = systems[secondary_sysID]
print('All System Keys:', list(systems.keys()))
print('Primary System Key:', primary_sysID)
print('System 1 IDs:', sys_1.id)
print('System 2 IDs:', sys_2.id)
# Calculate Useful Quantities
mass_ratio = sys_2.mass.sum() / sys_1.mass.sum()
total_mass = sys_1.mass.sum() + sys_2.mass.sum()
rel_pos = sys_1.center_of_mass() - sys_2.center_of_mass()
rel_vel = sys_1.center_of_mass_velocity() - sys_2.center_of_mass_velocity()
# Initialize Kepler Worker
kep = KeplerWorkerList[-1]
kep.initialize_from_dyn(total_mass, rel_pos[0], rel_pos[1], rel_pos[2],
rel_vel[0], rel_vel[1], rel_vel[2])
# Check to See if the Periastron is within the Ignore Distance for 10^3 Perturbation
p = kep.get_periastron()
ignore_distance = mass_ratio**(1. / 3.) * 600 | units.AU
if p > ignore_distance:
print("Encounter Ignored due to Periastron of", p.in_(units.AU),
"and an IgnoreDistance of", ignore_distance)
if KeplerWorkerList == None:
for K in KeplerWorkerList:
K.stop()
print("---------------------------------")
return None
# Move the Particles to be Relative to their Respective Center of Mass
cm_sys_1, cm_sys_2 = sys_1.center_of_mass(), sys_2.center_of_mass()
cmv_sys_1, cmv_sys_2 = sys_1.center_of_mass_velocity(
), sys_2.center_of_mass_velocity()
for particle in sys_1:
particle.position -= cm_sys_1
particle.velocity -= cmv_sys_1
for particle in sys_2:
particle.position -= cm_sys_2
particle.velocity -= cmv_sys_2
# Check to See if the Planets are Closer than the Ignore Distance
# Note: This shouldn't happen in the main code, but this prevents overshooting the periastron in debug mode.
if kep.get_separation() > ignore_distance:
kep.advance_to_radius(ignore_distance)
# Advance the Center of Masses to the Desired Distance in Reduced Mass Coordinates
x, y, z = kep.get_separation_vector()
rel_pos_f = rel_pos.copy()
rel_pos_f[0], rel_pos_f[1], rel_pos_f[2] = x, y, z
vx, vy, vz = kep.get_velocity_vector()
rel_vel_f = rel_vel.copy()
rel_vel_f[0], rel_vel_f[1], rel_vel_f[2] = vx, vy, vz
# Transform to Absolute Coordinates from Kepler Reduced Mass Coordinates
cm_pos_1, cm_pos_2 = sys_2.mass.sum(
) * rel_pos_f / total_mass, -sys_1.mass.sum() * rel_pos_f / total_mass
cm_vel_1, cm_vel_2 = sys_2.mass.sum(
) * rel_vel_f / total_mass, -sys_1.mass.sum() * rel_vel_f / total_mass
# Move the Particles to the New Postions of their Respective Center of Mass
for particle in sys_1:
particle.position += cm_pos_1
particle.velocity += cm_vel_1
for particle in sys_2:
particle.position += cm_pos_2
particle.velocity += cm_vel_2
# If not provided, stop Kepler and return the Systems as a Particle Set
if KeplerWorkerList == None:
for K in KeplerWorkerList:
K.stop()
# Collect the Collective Particle Set to be Returned Back
final_set = Particles()
final_set.add_particles(sys_1)
final_set.add_particles(sys_2)
print("---------------------------------")
return final_set
stopping_condition.enable()
sys.stdout.flush()
# Adding and Committing Particles to PH4
gravity.particles.add_particles(MasterSet)
gravity.commit_particles()
#print gravity.particles[-5:]
# Starting the AMUSE Channel for PH4
grav_to_MS_channel = gravity.particles.new_channel_to(MasterSet)
MS_to_grav_channel = MasterSet.new_channel_to(gravity.particles,
attributes=["x","y","z","vx","vy","vz"])
SmallScaleConverter = nbody_system.nbody_to_si(2*np.mean(MasterSet.mass), 2*np.mean(MasterSet.radius))
# Initializing Kepler and SmallN
kep = Kepler(unit_converter=SmallScaleConverter, redirection = "none")
kep.initialize_code()
util.init_smalln(unit_converter=SmallScaleConverter)
# Initializing MULTIPLES, Testing to See if a Crash Exists First
if read_from_file and crash:
time, multiples_code = read.recover_crash(crash_file, gravity, kep, util.new_smalln)
else:
multiples_code = multiples.Multiples(gravity, util.new_smalln, kep,
gravity_constant=units.constants.G)
multiples_code.neighbor_perturbation_limit = 0.05
#multiples_code.neighbor_distance_factor = 1.0
multiples_code.neighbor_veto = True
# Initializing Stellar Evolution (SeBa)
sev_code = SeBa()
def get_planetary_systems_from_set(bodies,
converter=None,
RelativePosition=False):
# Initialize Kepler
if converter == None:
converter = nbody_system.nbody_to_si(
bodies.mass.sum(),
2 * np.max(bodies.radius.number) | bodies.radius.unit)
kep_p = Kepler(unit_converter=converter, redirection='none')
kep_p.initialize_code()
kep_s = Kepler(unit_converter=converter, redirection='none')
kep_s.initialize_code()
# Seperate Out Planets and Stars from Bodies
stars, planets = util.get_stars(bodies), util.get_planets(bodies)
num_stars, num_planets = len(stars), len(planets)
# Initialize the Dictionary that Contains all Planetary Systems
systems = {}
# Start Looping Through Stars to Find Bound Planets
for star in stars:
system_id = star.id
#star.semimajor_axis, star.eccentricity, star.period, star.true_anomaly, star.mean_anomaly, star.kep_energy, star.angular_momentum = \
# None, None, None, None, None, None, None
current_system = systems.setdefault(system_id, Particles())
current_system.add_particle(star)
for planet in planets:
total_mass = star.mass + planet.mass
kep_pos = star.position - planet.position
kep_vel = star.velocity - planet.velocity
kep_p.initialize_from_dyn(total_mass, kep_pos[0], kep_pos[1],
kep_pos[2], kep_vel[0], kep_vel[1],
kep_vel[2])
a_p, e_p = kep_p.get_elements()
if e_p < 1.0:
# Check to See if The Stellar System is a Binary
# Note: Things get complicated if it is ...
noStellarHeirarchy = False
for other_star in (stars - star):
kep_s.initialize_from_dyn(
star.mass + other_star.mass, star.x - other_star.x,
star.y - other_star.y, star.z - other_star.z,
star.vx - other_star.vx, star.vy - other_star.vy,
star.vz - other_star.vz)
a_s, e_s = kep_s.get_elements()
r_apo = kep_s.get_apastron()
HillR = util.calc_HillRadius(a_s, e_s, other_star.mass,
star.mass)
if e_s >= 1.0 or HillR < r_apo:
noStellarHeirarchy = True
else:
noStellarHeirarchy = False
if noStellarHeirarchy:
# Get Additional Information on Orbit
planet.semimajor_axis = a_p
planet.eccentricity = e_p
planet.period = kep_p.get_period()
planet.true_anomaly, planet.mean_anomaly = kep_p.get_angles(
)
#planet.kep_energy, planet.angular_momentum = kep_p.get_integrals()
# Add the Planet to the System Set
current_system.add_particle(planet)
else:
# Handling for Planetary Systems in Stellar Heirarchical Structures
# Note: This is empty for now, maybe consider doing it by the heaviest bound stellar object as the primary.
pass
else:
continue
kep_p.stop()
kep_s.stop()
return systems
def new_kepler(self):
kepler = Kepler()
kepler.initialize_code()
return kepler
def run_ph4(infile = None, outfile = None,
number_of_stars = 100, number_of_binaries = 0,
end_time = 10 | nbody_system.time,
delta_t = 1 | nbody_system.time,
n_workers = 1, use_gpu = 1, gpu_worker = 1,
salpeter = 0,
accuracy_parameter = 0.1,
softening_length = 0.0 | nbody_system.length,
manage_encounters = 1, random_seed = 1234):
if random_seed <= 0:
numpy.random.seed()
random_seed = numpy.random.randint(1, pow(2,31)-1)
numpy.random.seed(random_seed)
print "random seed =", random_seed
if infile != None: print "input file =", infile
print "end_time =", end_time.number
print "delta_t =", delta_t.number
print "n_workers =", n_workers
print "use_gpu =", use_gpu
print "manage_encounters =", manage_encounters
print "\ninitializing the gravity module"
sys.stdout.flush()
init_smalln()
# Note that there are actually three GPU options:
#
# 1. use the GPU code and allow GPU use (default)
# 2. use the GPU code but disable GPU use (-g)
# 3. use the non-GPU code (-G)
if gpu_worker == 1:
try:
gravity = grav(number_of_workers = n_workers,
redirection = "none", mode = "gpu")
except Exception as ex:
gravity = grav(number_of_workers = n_workers,
redirection = "none")
else:
gravity = grav(number_of_workers = n_workers,
redirection = "none")
gravity.initialize_code()
gravity.parameters.set_defaults()
#-----------------------------------------------------------------
if infile == None:
print "making a Plummer model"
stars = new_plummer_model(number_of_stars)
id = numpy.arange(number_of_stars)
stars.id = id+1
print "setting particle masses and radii"
if salpeter == 0:
print 'equal masses'
total_mass = 1.0 | nbody_system.mass
scaled_mass = total_mass / number_of_stars
else:
print 'salpeter mass function'
scaled_mass = new_salpeter_mass_distribution_nbody(number_of_stars)
stars.mass = scaled_mass
print "centering stars"
stars.move_to_center()
print "scaling stars to virial equilibrium"
stars.scale_to_standard(smoothing_length_squared
= gravity.parameters.epsilon_squared)
else:
# Read the input data. Units are dynamical (sorry).
# Format: id mass pos[3] vel[3]
print "reading file", infile
id = []
mass = []
pos = []
vel = []
f = open(infile, 'r')
count = 0
for line in f:
if len(line) > 0:
count += 1
cols = line.split()
if count == 1: snap = int(cols[0])
elif count == 2: number_of_stars = int(cols[0])
elif count == 3: time = float(cols[0]) | nbody_system.time
else:
if len(cols) >= 8:
id.append(int(cols[0]))
mass.append(float(cols[1]))
pos.append((float(cols[2]),
float(cols[3]), float(cols[4])))
vel.append((float(cols[5]),
float(cols[6]), float(cols[7])))
f.close()
stars = datamodel.Particles(number_of_stars)
stars.id = id
stars.mass = mass | nbody_system.mass
stars.position = pos | nbody_system.length
stars.velocity = vel | nbody_system.speed
#stars.radius = 0. | nbody_system.length
total_mass = stars.mass.sum()
ke = pa.kinetic_energy(stars)
kT = ke/(1.5*number_of_stars)
if number_of_binaries > 0:
# Turn selected stars into binary components.
# Only tested for equal-mass case.
kep = Kepler(redirection = "none")
kep.initialize_code()
added_mass = 0.0 | nbody_system.mass
# Work with energies rather than semimajor axes.
Emin = 10*kT
Emax = 20*kT
ecc = 0.1
id_count = number_of_stars
nbin = 0
for i in range(0, number_of_stars,
number_of_stars/number_of_binaries):
# Star i is CM, becomes component, add other star at end.
nbin += 1
mass = stars[i].mass
new_mass = numpy.random.uniform()*mass # uniform q?
mbin = mass + new_mass
fac = new_mass/mbin
E = Emin + numpy.random.uniform()*(Emax-Emin)
a = 0.5*nbody_system.G*mass*new_mass/E
kep.initialize_from_elements(mbin, a, ecc)
dr = quantities.AdaptingVectorQuantity()
dr.extend(kep.get_separation_vector())
dv = quantities.AdaptingVectorQuantity()
dv.extend(kep.get_velocity_vector())
newstar = datamodel.Particles(1)
newstar.mass = new_mass
newstar.position = stars[i].position + (1-fac)*dr
newstar.velocity = stars[i].velocity + (1-fac)*dv
# stars[i].mass = mass
stars[i].position = stars[i].position - fac*dr
stars[i].velocity = stars[i].velocity - fac*dv
id_count += 1
newstar.id = id_count
stars.add_particles(newstar)
added_mass += new_mass
if nbin >= number_of_binaries: break
kep.stop()
print 'created', nbin, 'binaries'
sys.stdout.flush()
stars.mass = stars.mass * total_mass/(total_mass+added_mass)
number_of_stars += nbin
# Set dynamical radii (assuming virial equilibrium and standard
# units). Note that this choice should be refined, and updated
# as the system evolves. Probably the choice of radius should be
# made entirely in the multiples module. TODO. In these units,
# M = 1 and <v^2> = 0.5, so the mean 90-degree turnaround impact
# parameter is
#
# b_90 = G (m_1+m_2) / vrel^2
# = 2 <m> / 2<v^2>
# = 2 / N for equal masses
#
# Taking r_i = m_i / 2<v^2> = m_i in virial equilibrium means
# that, approximately, "contact" means a 90-degree deflection (r_1
# + r_2 = b_90). A more conservative choice with r_i less than
# this value will isolates encounters better, but also place more
# load on the large-N dynamical module.
stars.radius = stars.mass.number | nbody_system.length
time = 0.0 | nbody_system.time
# print "IDs:", stars.id.number
print "recentering stars"
stars.move_to_center()
sys.stdout.flush()
#-----------------------------------------------------------------
if softening_length < 0.0 | nbody_system.length:
# Use ~interparticle spacing. Assuming standard units here. TODO
eps2 = 0.25*(float(number_of_stars))**(-0.666667) \
| nbody_system.length**2
else:
eps2 = softening_length*softening_length
print 'softening length =', eps2.sqrt()
gravity.parameters.timestep_parameter = accuracy_parameter
gravity.parameters.epsilon_squared = eps2
gravity.parameters.use_gpu = use_gpu
# gravity.parameters.manage_encounters = manage_encounters
print ''
print "adding particles"
# print stars
sys.stdout.flush()
gravity.particles.add_particles(stars)
gravity.commit_particles()
print ''
print "number_of_stars =", number_of_stars
print "evolving to time =", end_time.number, \
"in steps of", delta_t.number
sys.stdout.flush()
# Channel to copy values from the code to the set in memory.
channel = gravity.particles.new_channel_to(stars)
stopping_condition = gravity.stopping_conditions.collision_detection
stopping_condition.enable()
# Debugging: prevent the multiples code from being called.
if 0:
stopping_condition.disable()
print 'stopping condition disabled'
sys.stdout.flush()
# -----------------------------------------------------------------
# Create the coupled code and integrate the system to the desired
# time, managing interactions internally.
kep = init_kepler(stars[0], stars[1])
multiples_code = multiples.Multiples(gravity, new_smalln, kep)
multiples_code.neighbor_perturbation_limit = 0.1
#multiples_code.neighbor_distance_factor = 1.0
#multiples_code.neighbor_veto = False
#multiples_code.neighbor_distance_factor = 2.0
multiples_code.neighbor_veto = True
print ''
print 'multiples_code.initial_scale_factor =', \
multiples_code.initial_scale_factor
print 'multiples_code.neighbor_perturbation_limit =', \
multiples_code.neighbor_perturbation_limit
print 'multiples_code.neighbor_veto =', \
multiples_code.neighbor_veto
print 'multiples_code.final_scale_factor =', \
multiples_code.final_scale_factor
print 'multiples_code.initial_scatter_factor =', \
multiples_code.initial_scatter_factor
print 'multiples_code.final_scatter_factor =', \
multiples_code.final_scatter_factor
print 'multiples_code.retain_binary_apocenter =', \
multiples_code.retain_binary_apocenter
print 'multiples_code.wide_perturbation_limit =', \
multiples_code.wide_perturbation_limit
pre = "%%% "
E0,cpu0 = print_log(pre, time, multiples_code)
while time < end_time:
time += delta_t
multiples_code.evolve_model(time)
# Copy values from the module to the set in memory.
channel.copy()
# Copy the index (ID) as used in the module to the id field in
# memory. The index is not copied by default, as different
# codes may have different indices for the same particle and
# we don't want to overwrite silently.
channel.copy_attribute("index_in_code", "id")
print_log(pre, time, multiples_code, E0, cpu0)
sys.stdout.flush()
#-----------------------------------------------------------------
if not outfile == None:
# Write data to a file.
f = open(outfile, 'w')
#--------------------------------------------------
# Need to save top-level stellar data and parameters.
# Need to save multiple data and parameters.
f.write('%.15g\n'%(time.number))
for s in multiples_code.stars: write_star(s, f)
#--------------------------------------------------
f.close()
print 'wrote file', outfile
print ''
gravity.stop()
def get_heirarchical_systems_from_set(bodies,
kepler_workers=None,
converter=None,
RelativePosition=False):
# Initialize Kepler
if kepler_workers == None:
if converter == None:
converter = nbody_system.nbody_to_si(
bodies.mass.sum(),
2 * np.max(bodies.radius.number) | bodies.radius.unit)
kep_p = Kepler(unit_converter=converter, redirection='none')
kep_p.initialize_code()
kep_s = Kepler(unit_converter=converter, redirection='none')
kep_s.initialize_code()
else:
kep_p = kepler_workers[0]
kep_s = kepler_workers[1]
# Seperate Out Planets and Stars from Bodies
stars, planets = util.get_stars(bodies), util.get_planets(bodies)
num_stars, num_planets = len(stars), len(planets)
# Initialize the Dictionary that Contains all Planetary Systems
systems = {}
# Initialize the List Used to Check Star IDs Against Already Classified Binaries
binary_ids = []
# Find Nearest Neighbors of the Set
closest_neighbours = stars.nearest_neighbour()
# Start Looping Through Stars to Find Bound Planets
for index, star in enumerate(stars):
# If the star is already in Binary_IDs, just go to the next star.
if star.id in binary_ids:
continue
# If not, Set the System ID and Set-up Data Structure.
system_id = star.id
current_system = systems.setdefault(system_id, Particles())
current_system.add_particle(star)
noStellarHierarchy = False
# If there is only one stars, there is obviously no stellar heirarchy in
# the encounter that is occuring.
if len(stars) == 1:
noStellarHierarchy = True
if not noStellarHierarchy:
# Check to see if the Nearest Neighbor is Mutual
star_neighbour_id = closest_neighbours[index].id
neighbour_neighbour_id = closest_neighbours[
stars.id == star_neighbour_id].id[0]
for other_star in (stars - star):
# Check to see if the two stars are bound.
kep_s.initialize_from_dyn(
star.mass + other_star.mass, star.x - other_star.x,
star.y - other_star.y, star.z - other_star.z,
star.vx - other_star.vx, star.vy - other_star.vy,
star.vz - other_star.vz)
a_s, e_s = kep_s.get_elements()
print(star.id, other_star.id, e_s)
# If they ARE NOT bound ...
if e_s >= 1.0:
noStellarHierarchy = True
# If they ARE bound ...
else:
# If the star is the star's neighbour's neighbour and visa-versa, then proceed.
print(star.id, other_star.id, star_neighbour_id,
neighbour_neighbour_id)
if star.id == neighbour_neighbour_id and other_star.id == star_neighbour_id:
noStellarHierarchy = False
print("Binary composed of Star", star.id, "and Star",
other_star.id, "has been detected!")
current_system.add_particle(other_star)
binary_ids.append(star.id)
binary_ids.append(other_star.id)
else:
print(
"!!! Alert: Bound Stars are not closest neighbours ..."
)
print("!!! Current Star:", star.id, "| Other Star:",
other_star.id)
print("!!! CS's Neighbour:", star_neighbour_id, \
"| CS's Neighbour's Neighbour:", neighbour_neighbour_id)
checked_planet_ids = []
for KeyID in systems.keys():
current_system = systems[KeyID]
sys_stars = util.get_stars(current_system)
noStellarHierarchy = False
# If there is only one stars, there is obviously no stellar heirarchy in
# the encounter that is occuring.
if len(sys_stars) == 1:
noStellarHierarchy = True
for planet in planets:
if planet.id in checked_planet_ids:
continue
star = sys_stars[sys_stars.id == KeyID][0]
total_mass = star.mass + planet.mass
kep_pos = star.position - planet.position
kep_vel = star.velocity - planet.velocity
kep_p.initialize_from_dyn(total_mass, kep_pos[0], kep_pos[1],
kep_pos[2], kep_vel[0], kep_vel[1],
kep_vel[2])
a_p, e_p = kep_p.get_elements()
P_p = kep_p.get_period()
Ta_p, Ma_p = kep_p.get_angles()
host_star_id = star.id
if e_p < 1.0:
# Check to See if The Planetary System is tied to a Stellar Binary
# Note: Things get complicated if it is ...
if noStellarHierarchy:
# Get Additional Information on Orbit
planet.semimajor_axis = a_p
planet.eccentricity = e_p
planet.period = P_p
planet.true_anomaly = Ta_p
planet.mean_anomaly = Ma_p
planet.host_star = star.id
# Add the Planet to the System Set
current_system.add_particle(planet)
else:
# Handling for Planetary Systems in Stellar Heirarchical Structures
# Note: We check to see which other star in the current systems
# have a better boundness with the planet and choose that
# as the new host star.
for other_star in sys_stars - star:
total_mass = other_star.mass + planet.mass
kep_pos = other_star.position - planet.position
kep_vel = other_star.velocity - planet.velocity
kep_p.initialize_from_dyn(total_mass, kep_pos[0],
kep_pos[1], kep_pos[2],
kep_vel[0], kep_vel[1],
kep_vel[2])
a_p2, e_p2 = kep_p.get_elements()
# Check to see if the planet is more bound to 'star' or
# 'other_star'. If its more bound to 'other_star',
# set the attributes to the more bound object. This will
# replace *_p with the better values with each loop.
if e_p2 < e_p:
a_p = a_p2
e_p = e_p2
P_p = kep_p.get_period()
Ta_p, Ma_p = kep_p.get_angles()
host_star_id = other_star.id
planet.semimajor_axis = a_p
planet.eccentricity = e_p
planet.period = P_p
planet.true_anomaly = Ta_p
planet.mean_anomaly = Ma_p
planet.host_star = host_star_id
# Add the Planet to the System Set
current_system.add_particle(planet)
checked_planet_ids.append(planet.id)
elif not noStellarHierarchy:
# Handling for Planetary Systems in Stellar Heirarchical Structures
# Note: We check to see which other star in the current systems
# have a better boundness with the planet and choose that
# as the new host star.
for other_star in sys_stars - star:
total_mass = other_star.mass + planet.mass
kep_pos = other_star.position - planet.position
kep_vel = other_star.velocity - planet.velocity
kep_p.initialize_from_dyn(total_mass, kep_pos[0],
kep_pos[1], kep_pos[2],
kep_vel[0], kep_vel[1],
kep_vel[2])
a_p2, e_p2 = kep_p.get_elements()
# Check to see if the planet is more bound to 'star' or
# 'other_star'. If its more bound to 'other_star',
# set the attributes to the more bound object. This will
# replace *_p with the better values with each loop.
if e_p2 < e_p:
a_p = a_p2
e_p = e_p2
P_p = kep_p.get_period()
Ta_p, Ma_p = kep_p.get_angles()
host_star_id = other_star.id
planet.semimajor_axis = a_p
planet.eccentricity = e_p
planet.period = P_p
planet.true_anomaly = Ta_p
planet.mean_anomaly = Ma_p
planet.host_star = host_star_id
# Add the Planet to the System Set
current_system.add_particle(planet)
else:
print(
"!!! Alert: Planet is not bound nor is it bound to any other star."
)
if kepler_workers == None:
kep_p.stop()
kep_s.stop()
return systems
def run_ph4(initial_file=None,
end_time=0 | nbody_system.time,
input_delta_t=0.0 | nbody_system.time,
input_Delta_t=1.0 | nbody_system.time,
input_timestep_parameter=0.0,
input_softening_length=-1.0 | nbody_system.length,
n_workers=1,
use_gpu=1,
gpu_worker=1,
use_multiples=True,
save_restart=False,
strict_restart=False):
# Read an N-body system from a file and run it to the specified
# time using the specified steps. Print log information and
# optionally save a restart file after every step. If the
# specified time is less than the time in the initial file, don't
# take a step, but still print out the log info. (Hence run_ph4
# also functions like Starlab sys_stats.)
print "initial_file =", initial_file
print "end_time =", end_time.number
print "n_workers =", n_workers
print "use_gpu =", use_gpu
print "use_multiples =", use_multiples
print "save_restart =", save_restart
print "strict_restart =", strict_restart
print "\ninitializing the gravity module"
sys.stdout.flush()
init_smalln()
# Note that there are actually three GPU options:
#
# 1. use the GPU code and allow GPU use (default)
# 2. use the GPU code but disable GPU use (-g)
# 3. use the non-GPU code (-G)
if gpu_worker == 1:
try:
gravity = grav(number_of_workers=n_workers,
redirection="none",
mode="gpu")
except Exception as ex:
gravity = grav(number_of_workers=n_workers, redirection="none")
else:
gravity = grav(number_of_workers=n_workers, redirection="none")
gravity.initialize_code()
gravity.parameters.set_defaults()
kep = Kepler(None, redirection="none")
kep.initialize_code()
stars, time, delta_t, E0, cpu0, multiples_code \
= read_state_from_file(initial_file, gravity, kep)
# Allow overrides of the restored data (OK for delta_t, NOT
# recommended for timestep_parameter or softening_length). Note
# that reading the state also commits the particles, and hence
# calculates the initial time steps. Probably should reinitialize
# if timestep_parameter or softening_length are changed. TODO
if input_delta_t.number > 0:
if input_delta_t != delta_t:
print 'modifying delta_t from stored', delta_t, \
'to input', input_delta_t
delta_t = input_delta_t
else:
print "using stored delta_t =", delta_t
print input_timestep_parameter
print gravity.parameters.timestep_parameter
if input_timestep_parameter > 0:
if input_timestep_parameter != gravity.parameters.timestep_parameter:
print 'modifying timestep_parameter from stored', \
gravity.parameters.timestep_parameter, \
'to input', input_timestep_parameter
gravity.parameters.timestep_parameter \
= input_timestep_parameter
else:
print 'timestep_parameter =', gravity.parameters.timestep_parameter
if input_softening_length.number >= 0:
if input_softening_length*input_softening_length \
!= gravity.parameters.epsilon_squared:
print 'modifying softening_length from stored', \
gravity.parameters.epsilon_squared.sqrt(), \
'to input', input_softening_length
gravity.parameters.epsilon_squared \
= softening_length*softening_length
else:
print 'softening length =', gravity.parameters.epsilon_squared.sqrt()
gravity.parameters.use_gpu = use_gpu
gravity.parameters.begin_time = time
if 0:
print ''
print gravity.parameters.begin_time
print stars.mass
#print stars.position
for s in stars:
print '%.18e %.18e %.18e' % (s.x.number, s.y.number, s.z.number)
print stars.velocity
channel = gravity.particles.new_channel_to(stars)
if use_multiples:
stopping_condition = gravity.stopping_conditions.collision_detection
stopping_condition.enable()
gravity.parameters.force_sync = 1 # end exactly at the specified time
pre = "%%% "
print_log(pre, time, multiples_code, E0, cpu0)
tsave = time + Delta_t
save_file = ''
while time < end_time:
time += delta_t
multiples_code.evolve_model(time) #, callback=handle_callback)
# Copy values from the module to the set in memory.
channel.copy()
# Copy the index (ID) as used in the module to the id field in
# memory. The index is not copied by default, as different
# codes may have different indices for the same particle and
# we don't want to overwrite silently.
channel.copy_attribute("index_in_code", "id")
# Write log information.
print_log(pre, time, multiples_code, E0, cpu0)
sys.stdout.flush()
# Optionally create a restart file.
if save_restart and time >= tsave:
#save_file = 't='+'{:07.2f}'.format(time.number) # not in Python 2.6
save_file = 't=%07.2f' % time.number
write_state_to_file(time, stars, gravity, multiples_code,
save_file, delta_t, E0, cpu0)
sys.stdout.flush()
tsave += Delta_t
if strict_restart: break
gravity.stop()
kep.stop()
stop_smalln()
return time, save_file
