Esempio n. 1
0
def sph_m_gen(fname,field_add):
    
    refined,dustdens,fc1,fw1,pf,ad = yt_octree_generate(fname,field_add)
    xmin = (fc1[:,0]-fw1[:,0]/2.).convert_to_units('cm') #in proper cm 
    xmax = (fc1[:,0]+fw1[:,0]/2.).convert_to_units('cm')
    ymin = (fc1[:,1]-fw1[:,1]/2.).convert_to_units('cm')
    ymax = (fc1[:,1]+fw1[:,1]/2.).convert_to_units('cm')
    zmin = (fc1[:,2]-fw1[:,2]/2.).convert_to_units('cm')
    zmax = (fc1[:,2]+fw1[:,2]/2.).convert_to_units('cm')
    

    #dx,dy,dz are the edges of the parent grid
    dx = (np.max(xmax)-np.min(xmin)).value
    dy = (np.max(ymax)-np.min(ymin)).value
    dz = (np.max(zmax)-np.min(zmin)).value


    xcent = np.mean([np.min(xmin),np.max(xmax)]) #kpc
    ycent = np.mean([np.min(ymin),np.max(ymax)])
    zcent = np.mean([np.min(zmin),np.max(zmax)])
    
    boost = np.array([xcent,ycent,zcent])
    print ('[pd_front end] boost = ',boost)

    
    #Tom Robitaille's conversion from z-first ordering (yt's default) to
    #x-first ordering (the script should work both ways)

    refined_array = np.array(refined)
    refined_array = np.squeeze(refined_array)
    
    order = find_order(refined_array)
    refined_reordered = []
    dustdens_reordered = np.zeros(len(order))
    
    
    
    for i in range(len(order)): 
        refined_reordered.append(refined[order[i]])
        dustdens_reordered[i] = dustdens[order[i]]


    refined = refined_reordered
    dustdens=dustdens_reordered

    #hyperion octree stats
    max_level = hos.hyperion_octree_stats(refined)


    pto.test_octree(refined,max_level)

    dump_cell_info(refined,fc1,fw1,xmin,xmax,ymin,ymax,zmin,zmax)
    np.save('refined.npy',refined)
    np.save('density.npy',dustdens)
    

    #========================================================================
    #Initialize Hyperion Model
    #========================================================================

    m = Model()
    
    if cfg.par.FORCE_RANDOM_SEED == True: m.set_seed(cfg.par.seed)

    print ('Setting Octree Grid with Parameters: ')



    #m.set_octree_grid(xcent,ycent,zcent,
    #                  dx,dy,dz,refined)
    m.set_octree_grid(0,0,0,dx/2,dy/2,dz/2,refined)    


    #get CMB:
    
    energy_density_absorbed=energy_density_absorbed_by_CMB()
    specific_energy = np.repeat(energy_density_absorbed.value,dustdens.shape)

    if cfg.par.PAH == True:
        
        # load PAH fractions for usg, vsg, and big (grain sizes)
        frac = cfg.par.PAH_frac

        # Normalize to 1
        total = np.sum(list(frac.values()))
        frac = {k: v / total for k, v in frac.items()}

        for size in frac.keys():
            d = SphericalDust(cfg.par.dustdir+'%s.hdf5'%size)
            if cfg.par.SUBLIMATION == True:
                d.set_sublimation_temperature('fast',temperature=cfg.par.SUBLIMATION_TEMPERATURE)
            #m.add_density_grid(dustdens * frac[size], cfg.par.dustdir+'%s.hdf5' % size)
            m.add_density_grid(dustdens*frac[size],d,specific_energy=specific_energy)
        m.set_enforce_energy_range(cfg.par.enforce_energy_range)
    else:
        d = SphericalDust(cfg.par.dustdir+cfg.par.dustfile)
        if cfg.par.SUBLIMATION == True:
            d.set_sublimation_temperature('fast',temperature=cfg.par.SUBLIMATION_TEMPERATURE)
        m.add_density_grid(dustdens,d,specific_energy=specific_energy)
        #m.add_density_grid(dustdens,cfg.par.dustdir+cfg.par.dustfile)  
    m.set_specific_energy_type('additional')








    return m,xcent,ycent,zcent,dx,dy,dz,pf,boost
Esempio n. 2
0
def sph_m_gen(fname,field_add):

    refined,dustdens,fc1,fw1,reg,ds = yt_octree_generate(fname,field_add)
    
    if float(yt.__version__[0:3]) >= 4:
        xmin = (fc1[:,0]-fw1[:,0]/2.).to('cm') #in proper cm 
        xmax = (fc1[:,0]+fw1[:,0]/2.).to('cm')
        ymin = (fc1[:,1]-fw1[:,1]/2.).to('cm')
        ymax = (fc1[:,1]+fw1[:,1]/2.).to('cm')
        zmin = (fc1[:,2]-fw1[:,2]/2.).to('cm')
        zmax = (fc1[:,2]+fw1[:,2]/2.).to('cm')
    else:
        xmin = (fc1[:,0]-fw1[:,0]/2.).convert_to_units('cm') #in proper cm
        xmax = (fc1[:,0]+fw1[:,0]/2.).convert_to_units('cm')
        ymin = (fc1[:,1]-fw1[:,1]/2.).convert_to_units('cm')
        ymax = (fc1[:,1]+fw1[:,1]/2.).convert_to_units('cm')
        zmin = (fc1[:,2]-fw1[:,2]/2.).convert_to_units('cm')
        zmax = (fc1[:,2]+fw1[:,2]/2.).convert_to_units('cm')

    #dx,dy,dz are the edges of the parent grid
    dx = (np.max(xmax)-np.min(xmin)).value
    dy = (np.max(ymax)-np.min(ymin)).value
    dz = (np.max(zmax)-np.min(zmin)).value


    xcent = float(ds.quan(cfg.model.x_cent,"code_length").to('cm').value)
    ycent = float(ds.quan(cfg.model.y_cent,"code_length").to('cm').value)
    zcent = float(ds.quan(cfg.model.z_cent,"code_length").to('cm').value)

    boost = np.array([xcent,ycent,zcent])
    print ('[sph_tributary] boost = ',boost)
    print ('[sph_tributary] xmin (pc)= ',np.min(xmin.to('pc')))
    print ('[sph_tributary] xmax (pc)= ',np.max(xmax.to('pc')))
    print ('[sph_tributary] ymin (pc)= ',np.min(ymin.to('pc')))
    print ('[sph_tributary] ymax (pc)= ',np.max(ymax.to('pc')))
    print ('[sph_tributary] zmin (pc)= ',np.min(zmin.to('pc')))
    print ('[sph_tributary] zmax (pc)= ',np.max(zmax.to('pc')))
    #Tom Robitaille's conversion from z-first ordering (yt's default) to
    #x-first ordering (the script should work both ways)



    refined_array = np.array(refined)
    refined_array = np.squeeze(refined_array)
    
    order = find_order(refined_array)
    refined_reordered = []
    dustdens_reordered = np.zeros(len(order))
    


    
    for i in range(len(order)): 
        refined_reordered.append(refined[order[i]])
        dustdens_reordered[i] = dustdens[order[i]]


    refined = refined_reordered
    dustdens=dustdens_reordered

    #hyperion octree stats
    max_level = hos.hyperion_octree_stats(refined)


    pto.test_octree(refined,max_level)
    
    if float(yt.__version__[0:3]) >= 4:
        dump_cell_info(refined,fc1.to('cm'),fw1.to('cm'),xmin,xmax,ymin,ymax,zmin,zmax)
    else:
        dump_cell_info(refined,fc1.convert_to_units('cm'),fw1.convert_to_units('cm'),xmin,xmax,ymin,ymax,zmin,zmax)
    
    np.save('refined.npy',refined)
    np.save('density.npy',dustdens)
    

    #========================================================================
    #Initialize Hyperion Model
    #========================================================================

    m = Model()
    
    #save in the m__dict__ that we're in an oct geometry
    m.__dict__['grid_type']='oct'

    print ('Setting Octree Grid with Parameters: ')



    #m.set_octree_grid(xcent,ycent,zcent,
    #                  dx,dy,dz,refined)
    m.set_octree_grid(0,0,0,dx/2,dy/2,dz/2,refined)    

    #get CMB:
    
    energy_density_absorbed=energy_density_absorbed_by_CMB()
    specific_energy = np.repeat(energy_density_absorbed.value,dustdens.shape)


    if cfg.par.otf_extinction == False:
        
        if cfg.par.PAH == True:

            # load PAH fractions for usg, vsg, and big (grain sizes)
            frac = cfg.par.PAH_frac
            
            # Normalize to 1
            total = np.sum(list(frac.values()))
            frac = {k: v / total for k, v in frac.items()}

            for size in frac.keys():
                d = SphericalDust(cfg.par.dustdir+'%s.hdf5'%size)
                if cfg.par.SUBLIMATION == True:
                    d.set_sublimation_temperature('fast',temperature=cfg.par.SUBLIMATION_TEMPERATURE)
                #m.add_density_grid(dustdens * frac[size], cfg.par.dustdir+'%s.hdf5' % size)
                m.add_density_grid(dustdens*frac[size],d,specific_energy=specific_energy)
            m.set_enforce_energy_range(cfg.par.enforce_energy_range)
        else:
            d = SphericalDust(cfg.par.dustdir+cfg.par.dustfile)
            if cfg.par.SUBLIMATION == True:
                d.set_sublimation_temperature('fast',temperature=cfg.par.SUBLIMATION_TEMPERATURE)
            m.add_density_grid(dustdens,d,specific_energy=specific_energy)
        #m.add_density_grid(dustdens,cfg.par.dustdir+cfg.par.dustfile)  


    else: #instead of using a constant extinction law across the
          #entire galaxy, we'll compute it on a cell-by-cell basis by
          #using information about the grain size distribution from
          #the simulation itself.


        print("==============================================\n")
        print("Entering OTF Extinction Calculation\n")
        print("Note: For very high-resolution grids, this may cause memory issues due to adding ncells dust grids")
        print("==============================================\n")
        
        ad = ds.all_data()
        nsizes = ad['PartType3','Dust_Size'].shape[1]
        ncells = reg.parameters["octree_of_sizes"].shape[0]
        #ensure that the grid has particles
        for isize in range(nsizes):
            try:
                assert (np.sum(reg.parameters["octree_of_sizes"][:,isize]) > 0)
            except AssertionError:
                raise AssertionError("[sph_tributary:] The grain size distribution smoothed onto the octree has deposited no particles.  Try either increasing your box size, or decreasing n_ref in parameters_master.  Alternatively, run the simulation with otf_extinction=False")

        #define the grid of sizes that will be used in tributary_dust_add
        grid_of_sizes = reg.parameters["octree_of_sizes"]
        
        active_dust_add(ds,m,grid_of_sizes,nsizes,dustdens,specific_energy,refined)
        

    m.set_specific_energy_type('additional')

    return m,xcent,ycent,zcent,dx,dy,dz,reg,ds,boost