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Alison_functions.py
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343 lines (324 loc) · 15.8 KB
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## Ali code
def write_MCFOST_parafile(parameters, MCFOST_path, file_name = "star.para"):
f = open(MCFOST_path + file_name, 'w')
f.write("4.0 mcfost version\n\n")
f.write("#Number of photon packages\n")
f.write(" " + parameters.nbr_photons_eq_th + " nbr_photons_eq_th : T computation\n")
f.write(" " + parameters.nbr_photons_lambda + " nbr_photons_lambda : SED computation\n")
f.write(" " + parameters.nbr_photons_image + " nbr_photons_image : images computation\n\n")
f.write("#Wavelength\n")
f.write(" " + parameters.n_lambda + " " + parameters.lambda_min + " " + parameters.lambda_max + " n_lambda, lambda_min, lambda_max [mum] Do not change this line unless you know what you are doing\n")
f.write(" " + parameters.compute_temp + " " + parameters.compute_sed + " " + parameters.default_wavelength + " compute temperature?, compute sed?, use parameters wavelength grid for output ?\n")
f.write(" " + parameters.wavelength_file + " wavelength file (if previous parameter is F)\n")
f.write(" " + parameters.separation_of_different_contributions + " " + parameters.stokes_parameters + " separation of different contributions?, stokes parameters?\n\n")
f.write("#Grid geometry and size\n")
f.write(" " + parameters.geometry + " 1 = cylindrical, 2 = spherical, 3 = Voronoi tessellation (this is in beta, please ask Christophe)\n")
f.write(" " + parameters.n_rad + " " + parameters.nz + " " + parameters.n_az + " " + parameters.n_rad_in + " n_rad (log distribution), nz (or n_theta), n_az, n_rad_in\n\n")
f.write("#Maps\n")
f.write(" " + parameters.grid_nx + " " + parameters.grid_ny + " " + parameters.size + " grid (nx,ny), size [AU]\n")
f.write(" " + parameters.imin + " " + parameters.imax + " " + parameters.n_incl + " " + parameters.centered + " RT: imin, imax, n_incl, centered ?\n")
f.write(" " + parameters.az_min + " " + parameters.az_max + " " + parameters.n_az_angles + " RT: az_min, az_max, n_az angles\n")
f.write(" " + parameters.distance + " distance (pc)\n")
f.write(" " + parameters.disk_PA + " disk PA\n\n")
f.write("#Scattering method\n")
f.write(" " + parameters.scattering_method + " 0=auto, 1=grain prop, 2=cell prop\n")
f.write(" " + parameters.mie_hg + " 1=Mie, 2=hg (2 implies the loss of polarizarion)\n\n")
f.write("#Symetries\n")
f.write(" " + parameters.image_symmetry + " image symmetry\n")
f.write(" " + parameters.central_symmetry + " central symmetry\n")
f.write(" " + parameters.axial_symmetry + " axial symmetry (important only if N_phi > 1)\n\n")
f.write("#Disk physics\n")
f.write(" " + parameters.dust_settling + " " + parameters.exp_strat + " " + parameters.a_strat + " dust_settling (0=no settling, 1=parametric, 2=Dubrulle, 3=Fromang), exp_strat, a_strat (for parametric settling)\n")
f.write(" " + parameters.dust_radial_migration + " dust radial migration\n")
f.write(" " + parameters.sublimate_dust + " sublimate dust\n")
f.write(" " + parameters.hydrostatic_equilibrium + " hydrostatic equilibrium\n")
f.write(" " + parameters.viscous_heating + " " + parameters.alpha_viscosity + " viscous heating, alpha_viscosity\n\n")
f.write("#Number of zones : 1 zone = 1 density structure + corresponding grain properties\n")
f.write(" " + parameters.number_of_zones + "\n\n")
f.write("#Density structure\n")
f.write(" " + parameters.zone_type + " zone type : 1 = disk, 2 = tappered-edge disk, 3 = envelope, 4 = debris disk, 5 = wall\n")
f.write(" " + parameters.dust_mass + " " + parameters.gas_to_dust_mass_ratio + " dust mass, gas-to-dust mass ratio\n")
f.write(" " + parameters.scale_height + " " + parameters.reference_radius + " " + parameters.vertical_profile_exponent + " scale height, reference radius (AU), unused for envelope, vertical profile exponent (only for debris disk)\n")
f.write(" " + parameters.Rin + " " + parameters.edge + " " + parameters.Rout + " " + parameters.Rc + " Rin, edge, Rout, Rc (AU) Rc is only used for tappered-edge & debris disks (Rout set to 8*Rc if Rout==0)\n")
f.write(" " + parameters.flaring_exponent + " flaring exponent, unused for envelope\n")
f.write(" " + parameters.surface_density_exponent + " " + parameters.negative_gamma_exp + " surface density exponent (or -gamma for tappered-edge disk or volume density for envelope), usually < 0, -gamma_exp (or alpha_in & alpha_out for debris disk)\n\n")
f.write("#Grain properties\n")
f.write(" " + parameters.number_of_species + " Number of species\n")
f.write(" " + parameters.grain_type + " " + parameters.N_components + " " + parameters.mixing_rule + " " + parameters.porosity + " " + parameters.max_fraction + " " + parameters.Vmax + " Grain type (Mie or DHS), N_components, mixing rule (1 = EMT or 2 = coating), porosity, mass fraction, Vmax (for DHS)\n")
f.write(" " + parameters.optical_indicies_file + " " + parameters.volume_fraction + " Optical indices file, volume fraction\n")
f.write(" " + parameters.heating_method + " Heating method : 1 = RE + LTE, 2 = RE + NLTE, 3 = NRE\n")
f.write(" " + parameters.amin + " " + parameters.amax + " " + parameters.aexp + " " + parameters.n_grains + " amin, amax [mum], aexp, n_grains (log distribution)\n\n")
f.write("#Molecular RT parameters\n")
f.write(" " + parameters.lpop + " " + parameters.laccurate_pop + " " + parameters.LTE + " " + parameters.profile_width + " lpop, laccurate_pop, LTE, profile width (km.s^-1)\n")
f.write(" " + parameters.v_turb + " v_turb (delta)\n")
f.write(" " + parameters.nmol + " nmol\n")
f.write(" " + parameters.molecular_data_filename + " " + parameters.level_max + " molecular data filename, level_max\n")
f.write(" " + parameters.vmax + " " + parameters.n_speed + " vmax (km.s^-1), n_speed\n")
f.write(" " + parameters.cst_molecule_abundance + " " + parameters.abundance + " " + parameters.abundance_file + " cst molecule abundance ?, abundance, abundance file\n")
f.write(" " + parameters.ray_tracing + " " + parameters.number_lines_in_RT + " ray tracing ?, number of lines in ray-tracing\n")
f.write(" " + parameters.transition_number_1 + " " + parameters.transition_number_2 + " " + parameters.transition_number_3 + " transition numbers\n\n")
f.write("#Atoms settings / share some informations with molecules\n")
f.write(" " + parameters.number_of_atoms + " #number of atoms\n" )
f.write(" " + parameters.all_levels + " #all levels treated in details at the moment\n" )
f.write(" " + parameters.non_LTE + " #non-LTE ?\n" )
f.write(" " + parameters.init_solution + " #initial solution, 0 LTE, 1 from file\n" )
f.write(" " + parameters.vmax + " " + parameters.n_points + " #vmax (km/s), n_points for ray-traced images and total flux\n" )
f.write(" " + parameters.images + " " + parameters.num_lines + " #images (T) or total flux (F) ? Number of lines for images\n" )
f.write(" " + parameters.upper_level + " " + parameters.lower_level + " #upper level -> lower level (Atomic model dependent)\n" )
f.write("#Star properties\n")
f.write(" " + parameters.number_of_stars + " Number of stars\n")
f.write(" " + parameters.temp + " " + parameters.radius + " " + parameters.mass + " " + parameters.x + " " + parameters.y + " " + parameters.z + " " + parameters.is_blackbody + " Temp, radius (solar radius),M (solar mass),x,y,z (AU), is a blackbody?\n")
f.write(" lte4000-3.5.NextGen.fits.gz\n")
f.write(" " + parameters.fUV + " " + parameters.slope_FUV + " fUV, slope_fUV\n")
f.close()
##
##
#
# class Default_parameters:
#
# def __init__(self):
# # number of photon packages
# self.nbr_photons_eq_th = "1.28e5"
# self.nbr_photons_lambda = "1.28e3"
# self.nbr_photons_image = "1.28e5"
#
# # wavelength
# # do not change these unless you know what you're doing
# self.n_lambda = "50"
# self.lambda_min = "0.1"
# self.lambda_max = "3000.0" # mum
#
# self.compute_temp = 'T'
# self.compute_sed = 'T'
# self.default_wavelength = 'T' # use default wavelength grid for output?
#
# self.wavelength_file = "IMLup.lambda" # if previous parameter is F
#
# self.separation_of_different_contributions = 'T'
# self.stokes_parameters = 'T'
#
# # grid geometry and size
# self.geometry = '1' # 1 = cylindrical, 2 = spherical, 3 = Voronoi tesselation (this is in beta, please ask Christophe)
#
# self.n_rad = "100" # log distribution
# self.nz = "70" # (or n_theta)
# self.n_az = "70"
# self.n_rad_in = "20"
#
# # maps
# self.grid_nx = "101"
# self.grid_ny = "101"
# self.size = "10." # AU
#
# # RT
# self.imin = "0."
# self.imax = "0."
# self.n_incl = "1"
# self.centered = 'F'
#
# self.az_min = "0"
# self.az_max = "0."
# self.n_az_angles = "1"
#
# self.distance = "140.0" # pc
# self.disk_PA = "-90."
#
# # Scattering method
# self.scattering_method = "0" # 0=auto, 1=grain prop, 2=cell prop
# self.mie_hg = "1" # 1=Mie, 2=hg (2 implies the loss of polarizarion)
#
# # Symmetries
# self.image_symmetry = 'F'
# self.central_symmetry = 'F'
# self.axial_symmetry = 'F' # (important only if N_phi > 1)
#
# # Disk physics
# self.dust_settling = "0" # (0=no settling, 1=parametric, 2=Dubrulle, 3=Fromang)
# self.exp_strat = "0.50"
# self.a_strat = "1.0" # (for parametric settling)
#
# self.dust_radial_migration = 'F'
# self.sublimate_dust = 'F'
# self.hydrostatic_equilibrium = 'F'
#
# self.viscous_heating = 'F'
# self.alpha_viscosity = "1e-5"
#
# # Number of zones: 1 zone = 1 density structure + corresponding grain properties
# self.number_of_zones = "1"
#
# # Density structure
# self.zone_type = "3" # zone type : 1 = disk, 2 = tappered-edge disk, 3 = envelope, 4 = debris disk, 5 = wall
#
# self.dust_mass = "1.e-6"
# self.gas_to_dust_mass_ratio = "100."
#
# self.scale_height = "10."
# self.reference_radius = "100.0" # AU, unused for envelope
# self.vertical_profile_exponent = "2" # only for debris disk
#
# self.Rin = "1.5"
# self.edge = "0.0"
# self.Rout = "50."
# self.Rc = "100." # AU, Rc is only used for tappered-edge & debris disks (Rout set to 8*Rc if Rout==0)
#
# self.flaring_exponent = "1.125" # unused for envelope
# self.surface_density_exponent = "-0.5" # (or -gamma for tappered-edge disk or volume density for envelope), usually < 0
# self.negative_gamma_exp = "0.0" # or alpha_in & alpha_out for debris disk
#
# # Grain properties
# self.number_of_species = "1"
#
# self.grain_type = "Mie" # Mie of DHS
# self.N_components = "1"
# self.mixing_rule = "2" # 1 = EMT or 2 = coating
# self.porosity = "0.0"
# self.max_fraction = "1.0"
# self.Vmax = "0.9" # for DHS
#
# self.optical_indicies_file = "Draine_Si_sUV.dat"
# self.volume_fraction = "1.0"
#
# self.heating_method = "1" # 1 = RE + LTE, 2 = RE + NLTE, 3 = NRE
#
# self.amin = "0.3" # mum
# self.amax = "0.3" # mum
# self.aexp = "3.5"
# self.n_grains = "100" # log distribution
#
# # Molecular RT settings
# self.lpop = 'T'
# self.laccurate_pop = 'T'
# self.LTE = 'T'
# self.profile_width = "15." # km.s^-1
#
# self.v_turb = "0.2" # delta
#
# self.nmol = "1"
#
# self.molecular_data_filename = "co@xpol.dat"
# self.level_max = "6"
#
# self.vmax = "10.0" # km.s^-1
# self.n_speed = "20"
#
# self.cst_molecule_abundance = 'T'
# self.abundance = "1.e-6"
# self.abundance_file = "abundance.fits.gz"
#
# self.ray_tracing = 'T'
# self.number_lines_in_RT = "2"
#
# self.transition_number_1 = "1"
# self.transition_number_2 = "2"
# self.transition_number_3 = "3"
#
#
#
# self.number_of_atoms = '1'
# self.all_levels = 'H_6.atom'
# self.non_LTE = 'F'
# self.init_solution = '0'
#
# self.vmax = '1000'
# self.n_points = '101'
# self.images = 'T'
# self.num_lines = '1'
# self.upper_level = '3'
# self.lower_level = '2'
#
#
#
#
# # Star properties
# self.number_of_stars = "1"
# self.temp = "4000.0"
# self.radius = "40" # solar radius
# self.mass = "1" # solar mass
# self.x = "0.0" # AU
# self.y = "0.0" # AU
# self.z = "0.0" # AU
# self.is_blackbody = 'T'
# self.fUV = "0.1"
# self.slope_FUV = "2.2"
#
# self.Rin = "1.0"
# self.edge = "0.0"
# self.Rout = "300."
# self.Rc = "100." # AU, Rc is only used for tappered-edge & debris disks (Rout set to 8*Rc if Rout==0)
#
# self.flaring_exponent = "1.125" # unused for envelope
#
# self.surface_density_exponent = "-0.5" # (or -gamma for tappered-edge disk or volume density for envelope), usually < 0
# self.negative_gamma_exp = "0.0" # or alpha_in & alpha_out for debris disk
#
# # Grain properties
# self.number_of_species = "1"
#
# self.grain_type = "Mie" # Mie of DHS
# self.N_components = "1"
# self.mixing_rule = "2" # 1 = EMT or 2 = coating
# self.porosity = "0.0"
# self.max_fraction = "1.0"
# self.Vmax = "0.9" # for DHS
#
# self.optical_indicies_file = "Draine_Si_sUV.dat"
# self.volume_fraction = "1.0"
#
# self.heating_method = "1" # 1 = RE + LTE, 2 = RE + NLTE, 3 = NRE
#
# self.amin = "0.03" # mum
# self.amax = "1000.0" # mum
# self.aexp = "3.5"
# self.n_grains = "100" # log distribution
#
# # Molecular RT settings
# self.lpop = 'T'
# self.laccurate_pop = 'T'
# self.LTE = 'T'
# self.profile_width = "15." # km.s^-1
#
# self.v_turb = "0.2" # delta
#
# self.nmol = "1"
#
# self.molecular_data_filename = "co@xpol.dat"
# self.level_max = "6"
#
# self.vmax = "1.0" # km.s^-1
# self.n_speed = "20"
#
# self.cst_molecule_abundance = 'T'
# self.abundance = "1.e-6"
# self.abundance_file = "abundance.fits.gz"
#
# self.ray_tracing = 'T'
# self.number_lines_in_RT = "3"
#
# self.transition_number_1 = "1"
# self.transition_number_2 = "2"
# self.transition_number_3 = "3"
#
# self.number_of_atoms = '1'
# self.all_levels = 'H_6.atom'
# self.non_LTE = 'F'
# self.init_solution = '0'
#
# self.vmax = '1000'
# self.n_points = '101'
# self.images = 'T'
# self.num_lines = '1'
# self.upper_level = '3'
# self.lower_level = '2'
#
# # Star properties
# self.number_of_stars = "1"
# self.temp = "4000.0"
# self.radius = "200.0" # solar radius
# self.mass = "1.0" # solar mass
# self.x = "0.0" # AU
# self.y = "0.0" # AU
# self.z = "0.0" # AU
# self.is_blackbody = 'T'
# self.fUV = "0.1"
# self.slope_FUV = "2.2"