textbook example code: molecular_cloud_collapse.pyΒΆ

[source code]

"""
  example of molecular cloud evolution with explictly
  split SPH and grav evolution

  Initial condition is a smooth spherical cloud with random velocities
  as in Bonnell et al. (2003)

"""

import numpy

from matplotlib import pyplot

from amuse.lab import *
from amuse.ext.molecular_cloud import molecular_cloud
from amuse.ext.evrard_test import body_centered_grid_unit_cube

from prepare_figure import single_frame, figure_frame, set_tickmarks
from distinct_colours import get_distinct

def make_map(sph,N=100,L=1):

    x,y=numpy.indices( ( N+1,N+1 ))

    x=L*(x.flatten()-N/2.)/N
    y=L*(y.flatten()-N/2.)/N
    z=x*0.
    vx=0.*x
    vy=0.*x
    vz=0.*x

    x=units.parsec(x)
    y=units.parsec(y)
    z=units.parsec(z)
    vx=units.kms(vx)
    vy=units.kms(vy)
    vz=units.kms(vz)

    rho,rhovx,rhovy,rhovz,rhoe=sph.get_hydro_state_at_point(x,y,z,vx,vy,vz)
    rho=rho.reshape((N+1,N+1))

    return rho

def write_output(filename, parts, conv):

    particles_nbody = ParticlesWithUnitsConverted(parts, conv.as_converter_from_nbody_to_si())

    write_set_to_file(particles_nbody, filename, "txt", attribute_names= ('rho', 'mass', 'x', 'y', 'z','vx', 'vy', 'vz'))

    return 0

def plot_hydro(time, sph, i, L=10):
    x_label = "x [pc]"
    y_label = "y [pc]"
    fig = single_frame(x_label, y_label, logx=False, logy=False, xsize=12, ysize=12)

#    fig=pyplot.figure(figsize=(12,12))

    rho=make_map(sph,N=200,L=L)
    pyplot.imshow(numpy.log10(1.e-5+rho.value_in(units.amu/units.cm**3)), extent=[-L/2,L/2,-L/2,L/2],vmin=1,vmax=5)
    pyplot.savefig("GMC_"+str(i)+".png")
#    subplot.set_title("GMC at zero age")
    #pyplot.title("Molecular cloud at time="+time.as_string_in(units.Myr))
    #pyplot.xlabel("x [pc]")
    #pyplot.ylabel("x [pc]")
    #pyplot.title("GMC at time="+time.as_string_in(units.Myr))
    #pyplot.savefig("GMC_"+str(i)+".png")


def run_molecular_cloud(N=100, Mcloud=100. | units.MSun, Rcloud=1. | units.parsec):

    conv = nbody_system.nbody_to_si(Mcloud,Rcloud)

    rho_cloud = 3.*Mcloud/(4.*numpy.pi*Rcloud**3)
    print rho_cloud
    tff = 0.5427/numpy.sqrt(constants.G*rho_cloud)
    print "t_ff=", tff.value_in(units.Myr), 'Myr'

    dt = 5.e-2 | units.Myr
    tend=1.0 | units.Myr

    parts=molecular_cloud(targetN=N,convert_nbody=conv,
            base_grid=body_centered_grid_unit_cube, seed=100).result

    #sph=Fi(conv, number_of_workers=3)
    sph=Fi(conv)
    sph.parameters.use_hydro_flag=True
    sph.parameters.radiation_flag=False
    sph.parameters.gamma=1
    sph.parameters.isothermal_flag=True
    sph.parameters.integrate_entropy_flag=False
    sph.parameters.timestep=dt
    sph.parameters.verbosity = 0
    sph.parameters.eps_is_h_flag = False# h_smooth is constant
    eps = 0.1 | units.parsec
    sph.parameters.gas_epsilon = eps
    sph.parameters.sph_h_const = eps
    parts.h_smooth= eps

    print 'eps-h flag', sph.get_eps_is_h(), sph.get_consthsm()

    expected_dt = 0.2*numpy.pi*numpy.power(eps, 1.5)/numpy.sqrt(constants.G*Mcloud/N)

    print "dt_exp=", expected_dt.value_in(units.Myr)
    print "dt=", dt
    print "eps=", sph.parameters.gas_epsilon.in_(units.parsec)

    sph.gas_particles.add_particles(parts)

    channel_from_sph_to_parts= sph.gas_particles.new_channel_to(parts)
    channel_from_parts_to_sph= parts.new_channel_to(sph.gas_particles)

    i=0
    L=6
    E0 = 0.0
    ttarget = 0.0 | units.Myr

    plot_hydro(ttarget, sph, i, L)

    while ttarget < tend:
        ttarget=float(i)*dt
        print ttarget
        sph.evolve_model(ttarget, timestep=dt)
        E = sph.gas_particles.kinetic_energy()+sph.gas_particles.potential_energy() + sph.gas_particles.thermal_energy()
        E_th = sph.gas_particles.thermal_energy()
        if i==0:
            E0 = E
        Eerr = (E-E0)/E0
        print 'energy=', E, 'energy_error=', Eerr, 'e_th=', E_th
        channel_from_sph_to_parts.copy()
        """
        filename = 'm400k_r10pc_e01_'+ str(i).zfill(2) + '.dat'
        print filename
        parts_sorted = parts.sorted_by_attribute('rho')
        write_output(filename, parts_sorted, conv)
        """
        plot_hydro(ttarget, sph, i, L)
        i=i+1

    sph.stop()
    return parts

if __name__ in ("__main__","__plot__"):

    parts = run_molecular_cloud(1000, Mcloud=10000. | units.MSun, Rcloud=3. | units.parsec)

Keywords: python, amuse, astrophysics, matplotlib, pylab, example, codex (see how-to-search-examples)