Python Model.add_spherical_source方法代码示例

# 需要导入模块: from hyperion.model import Model [as 别名]
# 或者: from hyperion.model.Model import add_spherical_source [as 别名]
# Model
m = Model()
dist = 20000 * au
x = np.linspace(-dist, dist, 101)
y = np.linspace(-dist, dist, 101)
z = np.linspace(-dist, dist, 101)
m.set_cartesian_grid(x,y,z)

# Dust
d = SphericalDust('kmh.hdf5')
d.set_sublimation_temperature('fast', temperature=1600.)
m.add_density_grid(np.ones((100,100,100)) * 1.e-18,'kmh.hdf5')

# Alpha centauri
sourceA = m.add_spherical_source()
sourceA.luminosity = 1.519 * lsun
sourceA.radius = 1.227 * rsun
sourceA.temperature = 5790.
sourceA.position = (0., 0., 0.)

# Beta centauri
sourceB = m.add_spherical_source()
sourceB.luminosity = 0.5 * lsun
sourceB.radius = 0.865 * rsun
sourceB.temperature = 5260.
sourceB.position = (-11.2 * au, 0., 0.)

# Proxima centauri
sourceP = m.add_spherical_source()
sourceP.luminosity = 0.0017 * lsun

# 需要导入模块: from hyperion.model import Model [as 别名]
# 或者: from hyperion.model.Model import add_spherical_source [as 别名]

#.........这里部分代码省略.........
            rho_dum = np.log10(rho_env_copy[(rc > 1.1*R_inf) & (np.isnan(rho_env_copy[:,ithetac]) == False),ithetac])
            rc_dum = np.log10(rc[(rc > 1.1*R_inf) & (np.isnan(rho_env_copy[:,ithetac]) == False)])
            rc_dum_nan = np.log10(rc[(rc > 1.1*R_inf) & (np.isnan(rho_env_copy[:,ithetac]) == True)])
            for i in range(0, len(rc_dum_nan)):
                rho_extrapol = poly(rc_dum, rho_dum, rc_dum_nan[i])
                rho_env_copy[(np.log10(rc) == rc_dum_nan[i]),ithetac] = 10**rho_extrapol
        rho_env2d = rho_env_copy
        rho_env = np.empty((nx,ny,nz))
        for i in range(0, nz):
            rho_env[:,:,i] = rho_env2d
        # create the array of density of disk and the whole structure
        #
        rho      = np.zeros([len(rc),len(thetac),len(phic)])
        # The function for calculating the normalization of disk using the total disk mass
        #
        for ir in range(0,len(rc)):
            for itheta in range(0,len(thetac)):
                for iphi in range(0,len(phic)):
                    if rc[ir] > rin_shell:
                        # Envelope profile
                        rho[ir,itheta,iphi] = rho_env[ir,itheta,iphi]
                    else:
                        rho[ir,itheta,iphi] = 1e-25
        rho_env  = rho_env  + 1e-40
        rho      = rho      + 1e-40

    # Call function to plot the density
    plot_density(rho, rc, thetac,'/Users/yaolun/bhr71/hyperion/', plotname='shell')
    # Insert the calculated grid and dust density profile into hyperion
    m.set_spherical_polar_grid(ri, thetai, phii)
    m.add_density_grid(rho.T, outdir+'oh5.hdf5')    # numpy read the array in reverse order

    # Define the luminsoity source
    source = m.add_spherical_source()
    source.luminosity = (4*PI*rstar**2)*sigma*(tstar**4)  # [ergs/s]
    source.radius = rstar  # [cm]
    source.temperature = tstar  # [K]
    source.position = (0., 0., 0.)
    print 'L_center =  % 5.2f L_sun' % ((4*PI*rstar**2)*sigma*(tstar**4)/LS)

    # Setting up the wavelength for monochromatic radiative transfer
    lambda0 = 0.1
    lambda1 = 2.0
    lambda2 = 50.0
    lambda3 = 95.0
    lambda4 = 200.0
    lambda5 = 314.0
    lambda6 = 670.0
    n01     = 10.0
    n12     = 20.0
    n23     = (lambda3-lambda2)/0.02
    n34     = (lambda4-lambda3)/0.03
    n45     = (lambda5-lambda4)/0.1
    n56     = (lambda6-lambda5)/0.1

    lam01   = lambda0 * (lambda1/lambda0)**(np.arange(n01)/n01)
    lam12   = lambda1 * (lambda2/lambda1)**(np.arange(n12)/n12)
    lam23   = lambda2 * (lambda3/lambda2)**(np.arange(n23)/n23)
    lam34   = lambda3 * (lambda4/lambda3)**(np.arange(n34)/n34)
    lam45   = lambda4 * (lambda5/lambda4)**(np.arange(n45)/n45)
    lam56   = lambda5 * (lambda6/lambda5)**(np.arange(n56+1)/n56)

    lam     = np.concatenate([lam01,lam12,lam23,lam34,lam45,lam56])
    nlam    = len(lam)

    # Create camera wavelength points

# 需要导入模块: from hyperion.model import Model [as 别名]
# 或者: from hyperion.model.Model import add_spherical_source [as 别名]
density[in_box] = rho_0

# Set up sphere 1
in_sphere_1 = (x - 10 * au) ** 2 + (y - 15 * au) ** 2 + (z - 20 * au) ** 2 < r_1 ** 2
density[in_sphere_1] = rho_1

# Set up sphere 2
in_sphere_2 = (x - 26.666667 * au) ** 2 + (y - 31.666667 * au) ** 2 + (z - 28.333333 * au) ** 2 < r_2 ** 2
density[in_sphere_2] = rho_2

# Remove dust close to source
in_rsub = np.sqrt(x * x + y * y + z * z) < RSUB
density[in_rsub] = 0.

m.add_density_grid(density, d)

# m.set_propagation_check_frequency(1.0)

# Set up illuminating source:
s = m.add_spherical_source()
s.radius = 6.6 * rsun
s.temperature = 33000.
s.luminosity = 4 * pi * s.radius ** 2 * sigma * s.temperature ** 4

# Set up number of photons
m.set_n_photons(initial=NPHOTONS, imaging=0)

# Write out and run
m.write(os.path.join('models', 'bm2_eff_vor_temperature.rtin'), overwrite=True)
m.run(os.path.join('models', 'bm2_eff_vor_temperature.rtout'), mpi=True, overwrite=True)

# 需要导入模块: from hyperion.model import Model [as 别名]
# 或者: from hyperion.model.Model import add_spherical_source [as 别名]

#.........这里部分代码省略.........
            R_disk_min = fix_params['R_min']*AU
            R_env_min  = fix_params['R_min']*AU

    # Make the Coordinates
    #
    ri           = rin * (rout/rin)**(np.arange(nx+1).astype(dtype='float')/float(nx))
    ri           = np.hstack((0.0, ri))
    thetai       = PI*np.arange(ny+1).astype(dtype='float')/float(ny)
    phii         = PI*2.0*np.arange(nz+1).astype(dtype='float')/float(nz)

    # Keep the constant cell size in r-direction at large radii
    #
    if max_rCell != None:
        ri_cellsize = ri[1:-1]-ri[0:-2]
        ind = np.where(ri_cellsize/AU > max_rCell)[0][0]       # The largest cell size is 100 AU
        ri = np.hstack((ri[0:ind],
                        ri[ind]+np.arange(np.ceil((rout-ri[ind])/max_rCell/AU))*max_rCell*AU))
        nxx = nx
        nx = len(ri)-1
    # Assign the coordinates of the center of cell as its coordinates.
    #
    rc           = 0.5*( ri[0:nx]     + ri[1:nx+1] )
    thetac       = 0.5*( thetai[0:ny] + thetai[1:ny+1] )
    phic         = 0.5*( phii[0:nz]   + phii[1:nz+1] )

    # for non-TSC model
    if ulrich:
        import hyperion as hp
        from hyperion.model import AnalyticalYSOModel

        non_tsc = AnalyticalYSOModel()

        # Define the luminsoity source
        nt_source = non_tsc.add_spherical_source()
        nt_source.luminosity = (4*PI*rstar**2)*sigma*(tstar**4)  # [ergs/s]
        nt_source.radius = rstar  # [cm]
        nt_source.temperature = tstar  # [K]
        nt_source.position = (0., 0., 0.)
        nt_source.mass = mstar

        # Envelope structure
        #
        nt_envelope = non_tsc.add_ulrich_envelope()
        nt_envelope.mdot = M_env_dot    # Infall rate
        nt_envelope.rmin = rin          # Inner radius
        nt_envelope.rc   = R_cen        # Centrifugal radius
        nt_envelope.rmax = R_env_max    # Outer radius
        nt_envelope.star = nt_source

        nt_grid = hp.grid.SphericalPolarGrid(ri, thetai, phii)

        rho_env_ulrich = nt_envelope.density(nt_grid).T
        rho_env_ulrich2d = np.sum(rho_env_ulrich**2, axis=2)/np.sum(rho_env_ulrich, axis=2)

    # Make the dust density model
    #
    # total mass counter
    total_mass = 0

    # normalization constant for cavity shape
    if theta_cav != 0:
        # using R = 10000 AU as the reference point
        c0 = (10000.*AU)**(-0.5)*\
             np.sqrt(1/np.sin(np.radians(theta_cav))**3-1/np.sin(np.radians(theta_cav)))
    else:
        c0 = 0

# 需要导入模块: from hyperion.model import Model [as 别名]
# 或者: from hyperion.model.Model import add_spherical_source [as 别名]
    def run_thermal_hyperion(self, nphot=1e6, mrw=False, pda=False, \
            niterations=20, percentile=99., absolute=2.0, relative=1.02, \
            max_interactions=1e8, mpi=False, nprocesses=None):
        d = []
        for i in range(len(self.grid.dust)):
            d.append(IsotropicDust( \
                    self.grid.dust[i].nu[::-1].astype(numpy.float64), \
                    self.grid.dust[i].albedo[::-1].astype(numpy.float64), \
                    self.grid.dust[i].kext[::-1].astype(numpy.float64)))

        m = HypModel()
        if (self.grid.coordsystem == "cartesian"):
            m.set_cartesian_grid(self.grid.w1*AU, self.grid.w2*AU, \
                    self.grid.w3*AU)
        elif (self.grid.coordsystem == "cylindrical"):
            m.set_cylindrical_polar_grid(self.grid.w1*AU, self.grid.w3*AU, \
                    self.grid.w2)
        elif (self.grid.coordsystem == "spherical"):
            m.set_spherical_polar_grid(self.grid.w1*AU, self.grid.w2, \
                    self.grid.w3)

        for i in range(len(self.grid.density)):
            if (self.grid.coordsystem == "cartesian"):
                m.add_density_grid(numpy.transpose(self.grid.density[i], \
                        axes=(2,1,0)), d[i])
            if (self.grid.coordsystem == "cylindrical"):
                m.add_density_grid(numpy.transpose(self.grid.density[i], \
                        axes=(1,2,0)), d[i])
            if (self.grid.coordsystem == "spherical"):
                m.add_density_grid(numpy.transpose(self.grid.density[i], \
                        axes=(2,1,0)), d[i])

        sources = []
        for i in range(len(self.grid.stars)):
            sources.append(m.add_spherical_source())
            sources[i].luminosity = self.grid.stars[i].luminosity * L_sun
            sources[i].radius = self.grid.stars[i].radius * R_sun
            sources[i].temperature = self.grid.stars[i].temperature

        m.set_mrw(mrw)
        m.set_pda(pda)
        m.set_max_interactions(max_interactions)
        m.set_n_initial_iterations(niterations)
        m.set_n_photons(initial=nphot, imaging=0)
        m.set_convergence(True, percentile=percentile, absolute=absolute, \
                relative=relative)

        m.write("temp.rtin")

        m.run("temp.rtout", mpi=mpi, n_processes=nprocesses)

        n = ModelOutput("temp.rtout")

        grid = n.get_quantities()

        self.grid.temperature = []
        temperature = grid.quantities['temperature']
        for i in range(len(temperature)):
            if (self.grid.coordsystem == "cartesian"):
                self.grid.temperature.append(numpy.transpose(temperature[i], \
                        axes=(2,1,0)))
            if (self.grid.coordsystem == "cylindrical"):
                self.grid.temperature.append(numpy.transpose(temperature[i], \
                        axes=(2,0,1)))
            if (self.grid.coordsystem == "spherical"):
                self.grid.temperature.append(numpy.transpose(temperature[i], \
                        axes=(2,1,0)))

        os.system("rm temp.rtin temp.rtout")

# 需要导入模块: from hyperion.model import Model [as 别名]
# 或者: from hyperion.model.Model import add_spherical_source [as 别名]

#.........这里部分代码省略.........
                        #                 else:
                        #                     mu_o_dum = roots[imu]
                        #         if mu_o_dum == -0.5:
                        #             print 'Problem with cubic solving, roots are: ', roots
                        #     mu_o = mu_o_dum.real
                        #     rho_env[ir,itheta,iphi] = M_env_dot/(4*PI*(G*mstar*rcen**3)**0.5)*(rc[ir]/rcen)**(-3./2)*(1+mu/mu_o)**(-0.5)*(mu/mu_o+2*mu_o**2*rcen/rc[ir])**(-1)
                        # # Disk profile
                        # if ((w >= R_disk_min) and (w <= R_disk_max)) == True:
                        #     h = ((w/(100*AU))**beta)*h100
                        #     rho_disk[ir,itheta,iphi] = rho_0*(1-np.sqrt(rstar/w))*(rstar/w)**(beta+1)*np.exp(-0.5*(z/h)**2)
                        # # Combine envelope and disk
                        # rho[ir,itheta,iphi] = rho_disk[ir,itheta,iphi] + rho_env[ir,itheta,iphi]
                    else:
                        rho[ir,itheta,iphi] = 1e-30
        rho_env  = rho_env  + 1e-40
        rho_disk = rho_disk + 1e-40
        rho      = rho      + 1e-40
    else:
        for ir in range(0,len(rc)):
            for itheta in range(0,len(thetac)):
                for iphi in range(0,len(phic)):
                    # Envelope profile
                    w = abs(rc[ir]*np.cos(thetac[itheta]))
                    z = rc[ir]*np.sin(thetac[itheta])
                    z_cav = c*abs(w)**1.5
                    z_cav_wall = c*abs(w-wall)**1.5
                    if z_cav == 0:
                        z_cav = R_env_max
                    if abs(z) > abs(z_cav):
                        # rho_env[ir,itheta,iphi] = rho_cav
                        # Modification for using density gradient in the cavity
                        if rc[ir] <= 20*AU:
                            rho_env[ir,itheta,iphi] = rho_cav_center*((rc[ir]/AU)**2)
                        else:
                            rho_env[ir,itheta,iphi] = rho_cav_center*discont*(20*AU/rc[ir])**2
                        i += 1
                    elif (abs(z) > abs(z_cav_wall)) and (abs(z) < abs(z_cav)):
                        rho_env[ir,itheta,iphi] = rho_wall
                    else:
                        j += 1
                        mu = abs(np.cos(thetac[itheta]))
                        mu_o = np.abs(fsolve(func,[0.5,0.5,0.5],args=(rc[ir],rcen,mu))[0])
                        rho_env[ir,itheta,iphi] = M_env_dot/(4*PI*(G*mstar*rcen**3)**0.5)*(rc[ir]/rcen)**(-3./2)*(1+mu/mu_o)**(-0.5)*(mu/mu_o+2*mu_o**2*rcen/rc[ir])**(-1)
                    # Disk profile
                    if ((w >= R_disk_min) and (w <= R_disk_max)) == True:
                        h = ((w/(100*AU))**beta)*h100
                        rho_disk[ir,itheta,iphi] = rho_0*(1-np.sqrt(rstar/w))*(rstar/w)**(beta+1)*np.exp(-0.5*(z/h)**2)
                    # Combine envelope and disk
                    rho[ir,itheta,iphi] = rho_disk[ir,itheta,iphi] + rho_env[ir,itheta,iphi]
        rho_env  = rho_env  + 1e-40
        rho_disk = rho_disk + 1e-40
        rho      = rho      + 1e-40

    # Insert the calculated grid and dust density profile into hyperion
    m.set_spherical_polar_grid(ri, thetai, phii)
    m.add_density_grid(rho.T, outdir+'oh5.hdf5')    # numpy read the array in reverse order

    # Define the luminsoity source
    source = m.add_spherical_source()
    source.luminosity = (4*PI*rstar**2)*sigma*(tstar**4)  # [ergs/s]
    source.radius = rstar  # [cm]
    source.temperature = tstar  # [K]
    source.position = (0., 0., 0.)
    print 'L_center =  % 5.2f L_sun' % ((4*PI*rstar**2)*sigma*(tstar**4)/LS)

    # Setting up images and SEDs
    image = m.add_peeled_images()
    image.set_wavelength_range(300, 2.0, 670.0)
    # pixel number
    image.set_image_size(300, 300)
    image.set_image_limits(-R_env_max, R_env_max, -R_env_max, R_env_max)
    image.set_viewing_angles([82.0], [0.0])
    image.set_uncertainties(True)
    # output as 64-bit
    image.set_output_bytes(8)

    # Radiative transfer setting

    # number of photons for temp and image
    m.set_raytracing(True)
    m.set_n_photons(initial=1000000, imaging=1000000, raytracing_sources=1000000, raytracing_dust=1000000)
    # number of iteration to compute dust specific energy (temperature)
    m.set_n_initial_iterations(5)
    m.set_convergence(True, percentile=99., absolute=1.5, relative=1.02)
    m.set_mrw(True)   # Gamma = 1 by default

    # Output setting
    # Density
    m.conf.output.output_density = 'last'

    # Density difference (shows where dust was destroyed)
    m.conf.output.output_density_diff = 'none'

    # Energy absorbed (using pathlengths)
    m.conf.output.output_specific_energy = 'last'

    # Number of unique photons that passed through the cell
    m.conf.output.output_n_photons = 'last'

    m.write(outdir+'old_setup2.rtin')

# 需要导入模块: from hyperion.model import Model [as 别名]
# 或者: from hyperion.model.Model import add_spherical_source [as 别名]

#.........这里部分代码省略.........

        # fix the tick label font
        ticks_font = mpl.font_manager.FontProperties(family='STIXGeneral',size=18)
        for label in ax.get_xticklabels():
            label.set_fontproperties(ticks_font)
        for label in ax.get_yticklabels():
            label.set_fontproperties(ticks_font)

        ax.set_ylim([0,15])
        fig.gca().set_xlim(left=np.log10(0.05))
        # ax.set_xlim([np.log10(0.8),np.log10(10000)])

        # subplot shows the radial density profile along the midplane
        ax_mid = plt.axes([0.2,0.2,0.2,0.2], frameon=True)
        ax_mid.plot(np.log10(rc/AU), np.log10(rho2d[:,199]/g2d/mmw/mh),'o',color='b',linewidth=1, markersize=2)
        ax_mid.plot(np.log10(rc/AU), np.log10(rho_env_tsc2d[:,199]/mmw/mh),'-',color='r',linewidth=1, markersize=2)
        # ax_mid.set_ylim([0,10])
        # ax_mid.set_xlim([np.log10(0.8),np.log10(10000)])
        ax_mid.set_ylim([0,15])
        fig.savefig(outdir+outname+'_gas_radial.pdf',format='pdf',dpi=300,bbox_inches='tight')
        fig.clf()

    # Insert the calculated grid and dust density profile into hyperion
    m.set_spherical_polar_grid(ri, thetai, phii)
    # temperary for comparing full TSC and infall-only TSC model
    # import sys
    # sys.path.append(os.path.expanduser('~')+'/programs/misc/')
    # from tsc_comparison import tsc_com
    # rho_tsc, rho_ulrich = tsc_com()
    m.add_density_grid(rho_dust.T, d)
    # m.add_density_grid(rho.T, outdir+'oh5.hdf5')    # numpy read the array in reverse order

    # Define the luminsoity source
    source = m.add_spherical_source()
    source.luminosity = (4*PI*rstar**2)*sigma*(tstar**4)  # [ergs/s]
    source.radius = rstar  # [cm]
    source.temperature = tstar  # [K]
    source.position = (0., 0., 0.)
    print 'L_center =  % 5.2f L_sun' % ((4*PI*rstar**2)*sigma*(tstar**4)/LS)

    # # add an infrared source at the center
    # L_IR = 0.04
    # ir_source = m.add_spherical_source()
    # ir_source.luminosity = L_IR*LS
    # ir_source.radius = rstar      # [cm]
    # ir_source.temperature = 500 # [K]  peak at 10 um
    # ir_source.position = (0., 0., 0.)
    # print 'Additional IR source, L_IR = %5.2f L_sun' % L_IR

    # Setting up the wavelength for monochromatic radiative transfer
    lambda0 = 0.1
    lambda1 = 2.0
    lambda2 = 50.0
    lambda3 = 95.0
    lambda4 = 200.0
    lambda5 = 314.0
    lambda6 = 1000.0
    n01     = 10.0
    n12     = 20.0
    n23     = 50.0

    lam01   = lambda0 * (lambda1/lambda0)**(np.arange(n01)/n01)
    lam12   = lambda1 * (lambda2/lambda1)**(np.arange(n12)/n12)
    lam23   = lambda2 * (lambda6/lambda2)**(np.arange(n23+1)/n23)

    lam      = np.concatenate([lam01,lam12,lam23])