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