This work by
Fujun Du is licensed
under a Creative Commons Attribution
4.0 International License.
Recently we have published a paper (see this link) that used this code.
You are welcome to contact me at fujun.du at gmail.com or fdu at umich.edu.
Go to the src directory. Inside it there is a makefile. You may
edit it for your own needs (but you don't have to). Then run
makeand an executable file with default name rac will be generated in the
same directory.
The makefile has a few options to compile in different environments.
- Gfortran higher than 4.6.2 or Intel Fortran higher than 12.1.5 (they are the version I have been using for developping the code).
- The cfitsio library.
There are a few input data files that are needed for the code to run.
The following files are compulsary:
1. Configuration file.
2. Chemical network.
3. Initial chemical composition.
4. Dust optical properties.
The following files are optional:
1. Density structure.
2. Enthalpy of formation of species.
3. Molecular transition data.
4. Stellar spectrum.
5. Locations to output the intermediate steps of chemcial evolution.
6. Species to output the intermediate steps of chemcial evolution.
7. Species to check for grid refinement.
By default all these files are in the inp directory, though they do not
have to. Go to this directory, and edit the file configure.dat to suit your
situation. It has about 200 entries. Some of them are for setting up the
physics and chemistry of the model, some are for setting up the running
environment, while others are switches telling the code whether or not it
should execute some specific tasks. Details for editing the configure file are
included below.
After you have get the configre file ready, and have all the needed files in
place, then open a terminal and go to the directory on top of inp, and
type in
src/rac ./inp/configure.dat
to start running the code.
With the template files that are already there the code should be able to run without any modification needed.
The configuration file is in the Fortran namelist format, so when editing
this file you may want to set the language type for syntax highlighting of your
editor to Fortran.
At the end of the configuration file you can write down any notes you want. Each inline comment must be preceded by a "!", and should be separated from the data content by at least one blank space. They will not be read by the code.
The following configuration file can be used to run a model (but will not do radiative transfer and ray-tracing to make images). To make images, see below.
! Filename: configure.dat
&grid_configure
grid_config%rmin = 1D-1 ! Grid inner boundary
grid_config%rmax = 200D0 ! Grid outer boundary
grid_config%zmin = 0D0 ! Grid lower boundary
grid_config%zmax = 200D0 ! Grid upper boundary
grid_config%dr0 = 2D-2 ! Width of the first r step
grid_config%columnwise = .true. ! Grid arranged in column manner
grid_config%ncol = 200 ! Number of columns
grid_config%use_data_file_input = .false. ! Whether to load structure from a data file
grid_config%analytical_to_use = 'Andrews' ! Analytical type; Andrews 2009
grid_config%interpolation_method = 'spline'
grid_config%max_ratio_to_be_uniform = 1.5D0 ! Determines the coarseness of the grid: highest/lowest within a grid cell
grid_config%density_scale = 8D0 ! Roughly the density scale you are interested in; log scale of cm-3; not very important
grid_config%density_log_range = 5D0 ! Range of density scale tou are interested in; not very important
grid_config%max_val_considered = 1d19 ! Not used
grid_config%min_val_considered = 1d1 ! Min density to be considered in the first few structure iterations
grid_config%min_val_considered_use = 1d3 ! Min density actually used
grid_config%very_small_len = 1D-6 ! Numerical accuracy of grid sizes; in AU
grid_config%smallest_cell_size = 2D-2 ! Grid cell size will not be smaller than this; in AU
grid_config%largest_cell_size = 10D0 ! Largest grid cell size; in AU
grid_config%largest_cell_size_frac = 1D-1 ! The grid cell size should not be larger than a faction of the distance to the central star
grid_config%small_len_frac = 5D-3 ! Similar to smallest_cell_size, but in a fractional sense
grid_config%refine_at_r0_in_exp = .false. ! Whether to refine the grid at r0, where the disk structure makes a transition; r0 is set in later sections
/
&chemistry_configure
chemsol_params%dt_first_step = 1D-8 ! The first time step in year; time steps for chemical evolution is logarithmic
chemsol_params%t_max = 1D6 ! Final time
chemsol_params%ratio_tstep = 1.1D0 ! Ratio between width of the time steps
chemsol_params%max_runtime_allowed = 60.0 ! Max CPU time for each time step
chemsol_params%RTOL = 1D-4 ! Relative tolerance of the result (abundances); for the ODE solver
chemsol_params%ATOL = 1D-30 ! Absolute tolerance of the result
chemsol_params%mxstep_per_interval = 6000 ! Max number of steps for each time interval
chemsol_params%chem_files_dir = './inp/' ! Directory of the chemical reaction files
chemsol_params%filename_chemical_network = 'rate06_withgrain_lowH2Bind_hiOBind_lowCObind.dat'
chemsol_params%filename_initial_abundances = 'ini_abund_waterice_loMetal_CO.dat'
chemsol_params%filename_species_enthalpy = 'Species_enthalpy.dat' ! Affect the chemical heating and cooling rates
chemsol_params%H2_form_use_moeq = .false. ! Which kind of formula to use for the formation rate of H2; usually just set to false
chemsol_params%flag_chem_evol_save = .false. ! Whether to save the chemical abundances at each time step; its content is overwritten at the next time step
chemsol_params%evol_dust_size = .false. ! Not well implemented; whether to evolve the dust grain size
chemsol_params%steps_reset_solver = 50 ! For the solver; reset the solver after this number of steps
/
&heating_cooling_configure
! When use_analytical_CII_OI is true, the two files will not be used.
heating_cooling_config%dir_transition_rates = './transitions/' ! Directory for the radiative files
heating_cooling_config%use_analytical_CII_OI = .true. ! Whether to use analytical formula for CII and OI cooling
heating_cooling_config%filename_CII = '' ! Cooling rates filename when not using analytical formula
heating_cooling_config%filename_OI = ''
heating_cooling_config%IonCoolingWithLut = .true. ! What kind of formula to use for ion cooling
heating_cooling_config%filename_NII = 'N+_LUT.bin'
heating_cooling_config%filename_SiII = 'Si+_LUT.bin'
heating_cooling_config%filename_FeII = 'Fe+_LUT.bin'
heating_cooling_config%solve_method = 2 ! Which method to use for calculating the statistical equilibrium for radiative cooling; 1: ODE; 2: Newton
heating_cooling_config%use_mygasgraincooling = .true. ! What kind of formula to use for calculating gas-grain collisional cooling; if true, use a more accurate form
heating_cooling_config%use_chemicalheatingcooling = .true. ! Whether to include chemical heating/cooling
heating_cooling_config%use_Xray_heating = .true. ! Whether to include X-ray heating
heating_cooling_config%heating_Xray_en = 0.0D0 ! Ignored
heating_cooling_config%heating_eff_chem = 0.3D0 ! Efficiency for chemical heating/cooling
heating_cooling_config%heating_eff_H2form = 0.5D0 ! Efficiency for H2 formation heating
heating_cooling_config%heating_eff_phd_H2 = 1D0 ! Efficiency for H2 photodissiation heating
heating_cooling_config%heating_eff_phd_H2O = 0.5D0 ! Efficiency for water photodissiation heating
heating_cooling_config%heating_eff_phd_OH = 0.5D0 ! Efficiency for OH photodissiation heating
heating_cooling_config%cooling_gg_coeff = 1D0 ! Efficiency for gas-grain collisional cooling
/
&montecarlo_configure
mc_conf%nph = 4000000 ! Number of photon packets; divide total star luminosity into this number
mc_conf%nmax_cross = 1999999999 ! Max num of cell crossing before any absorption or scattering for a photon
mc_conf%nmax_encounter = 1999999999 ! Max num of absorption and scattering events for a photon
mc_conf%ph_init_symmetric = .true. ! Mirror the upper disk and lower disk above and below the midplane
mc_conf%refine_UV = 2D-1 ! Refine for the UV photons; use smaller energy packets for them so that they have better statistics
mc_conf%refine_LyA = 1D-1
mc_conf%refine_Xray = 1D-3
mc_conf%disallow_any_scattering = .false. ! If true, there will be no scattering
mc_conf%mc_dir_in = './inp/' ! Input directory for some needed data
mc_conf%mc_dir_out = 'mc/'
mc_conf%fname_photons = 'escaped_photons.dat' ! Parameters for each escaped photon are saved in this file
mc_conf%fname_water = 'H2O.photoxs' ! Water absorption cross section
mc_conf%fname_star = 'tw_hya_spec_combined.dat' ! Input stellar spectrum
mc_conf%collect_photon = .true. ! The collected photons can be utilized to make an SED
mc_conf%collect_lam_min = 1D0 ! Minimum lambda; in angstrom
mc_conf%collect_lam_max = 1D8
mc_conf%collect_nmu = 4 ! Number of directions to collect photons
mc_conf%collect_ang_mins = 0D0 4D0 40D0 80D0 ! Ranges of angles (observing direction) to collect photons
mc_conf%collect_ang_maxs = 3D0 10D0 50D0 90D0
mc_conf%nlen_lut = 2048 ! Size of the look-up table for the dust optical parameters needed by the radiative transfer
mc_conf%TdustMin = 1D0 ! Lowest temperature allowed for the dust grains; in K
mc_conf%TdustMax = 2D3 ! Highest temperature allowed for the dust grains
mc_conf%use_blackbody_star = .false. ! Whether to use blackbody spectrum for the star
mc_conf%dist = 51.0D0 ! Distance of the source in pc
/
&dustmix_configure ! To make different dust compositions
dustmix_info%nmixture = 2 ! Number of mixtures you want to make; max: 4
dustmix_info%lam_min = 1D-4 ! Minimum wavelength (micron) to be considered
dustmix_info%lam_max = 1D4 ! Maximum ...
!
dustmix_info%mix(1)%id = 1 ! Mixture 1
dustmix_info%mix(1)%nrawdust = 3 ! Number of raw material for mixing
dustmix_info%mix(1)%rho = 3D0 ! Dust material density in g cm-3
dustmix_info%mix(1)%dir = './inp/'
dustmix_info%mix(1)%filenames(1) = 'silicate_draine.opti' ! Filename of raw material 1
dustmix_info%mix(1)%filenames(2) = 'graphite_draine_pa_0.1.opti'
dustmix_info%mix(1)%filenames(3) = 'graphite_draine_pe_0.1.opti'
dustmix_info%mix(1)%weights(1) = 0.8D0 ! Weight of raw material 1
dustmix_info%mix(1)%weights(2) = 0.04D0
dustmix_info%mix(1)%weights(3) = 0.16D0
!
dustmix_info%mix(2)%id = 2 ! Mixture 1
dustmix_info%mix(2)%nrawdust = 1 ! Number of raw material for mixing
dustmix_info%mix(2)%rho = 3D0 ! Dust material density in g cm-3
dustmix_info%mix(2)%dir = './inp/'
dustmix_info%mix(2)%filenames(1) = 'silicate_draine.opti' ! Filename of raw material 1
dustmix_info%mix(2)%weights(1) = 1.0D0 ! Weight of raw material 1
/
&disk_configure
a_disk%star_mass_in_Msun = 0.6D0 ! Mass of the central star
a_disk%star_radius_in_Rsun = 1D0 ! Radius of the central star
a_disk%star_temperature = 4000D0 ! Surface temperature of the star
a_disk%T_Xray = 1D7 ! Equivalent blackbody tempearture for the X-ray spectrum of the star
a_disk%E0_Xray = 0.1D0 ! Lower limit of the X-ray spectrum in keV
a_disk%E1_Xray = 10D0 ! Upper limit of the X-ray spectrum in keV
a_disk%lumi_Xray = 1.6D30 ! Total X-ray luminosity of the star; in erg/s
a_disk%starpos_r = 0D0 ! Position of the star
a_disk%starpos_z = 0D0
!
a_disk%use_fixed_alpha_visc = .false. ! If false, the alpha is not fixed
a_disk%allow_gas_dust_en_exch = .false. ! Whether to let dust transfer energy back to gas; not well-implemented
a_disk%base_alpha = 0.01D0 ! Maximum alpha
!
a_disk%Tdust_iter_tandem = .false. ! Whether to evolve the dust temperature; not well-implemented
!
a_disk%waterShieldWithRadTran = .true. ! True means water shielding is included during the Monte Carlo radiative transfer
!
a_disk%andrews_gas%useNumDens = .true. ! Gas density is the number density of hydrogen nuclei
a_disk%andrews_gas%Md = 2D-2 ! Total mass in Msun
a_disk%andrews_gas%rin = 1D-1 ! Inner edge; can be different from rmin of grid_config; in AU
a_disk%andrews_gas%rout = 200D0 ! Outer edge
a_disk%andrews_gas%rc = 80D0 ! Characteristic radius; see Andrews 2009
a_disk%andrews_gas%hc = 10D0 ! Scale height at boundary
a_disk%andrews_gas%gam = 1.5D0 ! Power index
a_disk%andrews_gas%psi = 1.0D0 !
a_disk%andrews_gas%r0_in_exp = 3.5D0 ! Inward tapering; the starting radius; in AU
a_disk%andrews_gas%rs_in_exp = 1D2 ! Radius scale for the tapering; in AU; very large value means a simple cutoff
a_disk%andrews_gas%f_in_exp = 1D-5 ! Constant scaling factor
!
a_disk%ndustcompo = 3 ! Number of dust components
!
a_disk%dustcompo(1)%itype = 1 ! Dust mixture type to use
a_disk%dustcompo(1)%mrn%rmin = 5D-3 ! Min radius; in micron
a_disk%dustcompo(1)%mrn%rmax = 1D3 ! Max radius
a_disk%dustcompo(1)%mrn%n = 3.5D0 ! Power index for the dust grain size distribution
a_disk%dustcompo(1)%andrews%useNumDens = .false. ! Use mass density insteady of number density
a_disk%dustcompo(1)%andrews%Md = 4D-4 ! Total mass in this dust component; in solar mass
a_disk%dustcompo(1)%andrews%rin = 1D0 ! Spatial distribution of the dust
a_disk%dustcompo(1)%andrews%rout = 200D0
a_disk%dustcompo(1)%andrews%rc = 40D0
a_disk%dustcompo(1)%andrews%hc = 3D0
a_disk%dustcompo(1)%andrews%gam = 1.5D0
a_disk%dustcompo(1)%andrews%psi = 1.0D0
a_disk%dustcompo(1)%andrews%r0_in_exp = 3.5D0
a_disk%dustcompo(1)%andrews%rs_in_exp = 0.5D0
a_disk%dustcompo(1)%andrews%p_in_exp = 3D0
a_disk%dustcompo(1)%andrews%f_in_exp = 1D0
a_disk%dustcompo(1)%andrews%r0_out_exp = 45D0 ! Outer tapering; in AU
a_disk%dustcompo(1)%andrews%rs_out_exp = 5D0
a_disk%dustcompo(1)%andrews%f_out_exp = 1D0
!
a_disk%dustcompo(2)%itype = 1 ! Dust mixture type to use
a_disk%dustcompo(2)%mrn%rmin = 5D-3 ! Min radius
a_disk%dustcompo(2)%mrn%rmax = 1D0 ! Max radius
a_disk%dustcompo(2)%mrn%n = 3.5D0 ! Power index
a_disk%dustcompo(2)%andrews%useNumDens = .false. ! Use mass density insteady of number density
a_disk%dustcompo(2)%andrews%Md = 2D-5
a_disk%dustcompo(2)%andrews%rin = 1D-1
a_disk%dustcompo(2)%andrews%rout = 200D0
a_disk%dustcompo(2)%andrews%rc = 80D0
a_disk%dustcompo(2)%andrews%hc = 20D0
a_disk%dustcompo(2)%andrews%gam = 0.5D0
a_disk%dustcompo(2)%andrews%psi = 1.0D0
a_disk%dustcompo(2)%andrews%r0_in_exp = 3.5D0
a_disk%dustcompo(2)%andrews%rs_in_exp = 0.5D0
a_disk%dustcompo(2)%andrews%p_in_exp = 3D0
a_disk%dustcompo(2)%andrews%f_in_exp = 1D0
!
a_disk%dustcompo(3)%itype = 2 ! Dust mixture type to use
a_disk%dustcompo(3)%mrn%rmin = 0.9D0 ! Min radius
a_disk%dustcompo(3)%mrn%rmax = 2D0 ! Max radius
a_disk%dustcompo(3)%mrn%n = 3.5D0 ! Power index
a_disk%dustcompo(3)%andrews%useNumDens = .false. ! Use mass density insteady of number density
a_disk%dustcompo(3)%andrews%Md = 1D-9
a_disk%dustcompo(3)%andrews%rin = 1D-1
a_disk%dustcompo(3)%andrews%rout = 3.5D0
a_disk%dustcompo(3)%andrews%rc = 80D0
a_disk%dustcompo(3)%andrews%hc = 10D0
a_disk%dustcompo(3)%andrews%gam = 1.0D0
a_disk%dustcompo(3)%andrews%psi = 1.0D0
a_disk%dustcompo(3)%andrews%r0_in_exp = 0.4D0
a_disk%dustcompo(3)%andrews%rs_in_exp = 0.1D0
a_disk%dustcompo(3)%andrews%p_in_exp = 2D0
a_disk%dustcompo(3)%andrews%f_in_exp = 1D0
/
&raytracing_configure ! Not needed when you don't do ray-tracing calculations (to generate spectra and images)
raytracing_conf%dirname_mol_data = './transitions/' ! Directory for the radiative transfer parameters
raytracing_conf%fname_mol_data = '12C16O_H2.dat' ! Filename of the transition rates
raytracing_conf%line_database = 'lamda' ! Data format
raytracing_conf%mole_name_disp = 'C$^{18}$O' ! Actually calculating for C18O, so use this name
raytracing_conf%maxx = 2.0000e+02 ! For making images; box size in AU; (-maxx, maxx)
raytracing_conf%maxy = 2.0000e+02
raytracing_conf%nx = 401 ! Number of pixels in each direction
raytracing_conf%ny = 401
raytracing_conf%nfreq_window = 3 ! Only care about lines within these frequency windows
raytracing_conf%freq_mins = 0.9D11 3.4D11 6.90D11 ! Ranges of the frequency windows; in Hz
raytracing_conf%freq_maxs = 3.0D11 3.6D11 6.92D11
raytracing_conf%nf = 200 ! Number of spectral channels
raytracing_conf%VeloKepler = 3D4 ! A rough estimation of the highest Keplerian velocity in m/s; for calculating the line velocity range
raytracing_conf%E_min = 0D0 ! Range of energy level of transitions we care about; in K
raytracing_conf%E_max = 3D3
raytracing_conf%min_flux = 0D-2 ! Minimum line flux to be saved; in Jy
raytracing_conf%save_spectrum_only = .false. ! If true, the image will not be saved; only the total spectrum is saved
raytracing_conf%nlam_window = 6 ! Only for continuum; make continuum spectra in these wavelength ranges; in micron
raytracing_conf%lam_mins = 1D-4 1D-3 0.1 1.0 10.0 100.0
raytracing_conf%lam_maxs = 1D-3 1D-2 1.0 10.0 100.0 1000.0
raytracing_conf%nlam = 100 ! Lambda channels
raytracing_conf%abundance_factor = 2.0D-3 ! For modeling isotopologues when the transition rates of itself is not available
raytracing_conf%useLTE = .true. ! Whether use LTE
raytracing_conf%nth = 1 ! Number of viewing angles (theta)
raytracing_conf%view_thetas = 7.0000e+00 ! Viewing angles in degree
raytracing_conf%dist = 5.1000e+01 ! Distance of the source in pc
raytracing_conf%VeloTurb = 200D0 ! Turbulent line broadening; in m/s
raytracing_conf%VeloWidth = 30D0 ! Additional velocity width added to the spectra velocity range; in m/s
/
&cell_configure
cell_params_ini%omega_albedo = 0.5D0 ! Dust albedo, only for chemistry
cell_params_ini%UV_G0_factor_background = 1D0 ! ISM UV
cell_params_ini%zeta_cosmicray_H2 = 1.36D-17 ! Cosmic ray intensity
cell_params_ini%PAH_abundance = 1.6D-9 ! PAH abundance; for heating/cooling
cell_params_ini%GrainMaterialDensity_CGS = 2D0 ! Density of dust material; not used
cell_params_ini%MeanMolWeight = 1.4D0 ! Mean molecular weight of the gas
cell_params_ini%alpha_viscosity = 0.01D0 ! Alpha; not used
/
&analyse_configure
! Do chemical analysis for some species at some locations
a_disk_ana_params%do_analyse = .true.
a_disk_ana_params%analyse_points_inp_dir = './inp/'
a_disk_ana_params%file_list_analyse_points = 'points_to_analyse.dat'
a_disk_ana_params%file_list_analyse_species = 'Species_to_analyse.dat'
a_disk_ana_params%file_analyse_res_ele = 'elemental_reservoir.dat' ! Which species contain the most of one element
a_disk_ana_params%file_analyse_res_contri = 'contributions.dat' ! Which reactions are the most important for the creation and destruction of each species
/
&iteration_configure
a_disk_iter_params%n_iter = 1 ! Number of iterations
a_disk_iter_params%nlocal_iter = 4 ! For numerical stability
a_disk_iter_params%do_vertical_struct = .true. ! Whether do the vertical structure calculation
a_disk_iter_params%do_vertical_with_Tdust = .true. ! Whether to use dust temperature for vertical structure calculation
a_disk_iter_params%calc_Av_toStar_from_Ncol = .false. ! Whether to calculate Av by the column density from each location towards the star
a_disk_iter_params%calc_zetaXray_from_Ncol = .false. ! Whether to calculate X-ray ionization rate based on the column density from each location towards the star
!
a_disk_iter_params%rescale_ngas_2_rhodust = .true. ! If true, the gas density is a simple scaling of the dust density
a_disk_iter_params%dust2gas_mass_ratio_deflt = 1.0D-2 ! Dust-to-gas mass ratio used for calculating the gas density from the dust density using simple scaling
a_disk_iter_params%max_num_of_cells = 10000 ! Maximum number of grid cells
!
a_disk_iter_params%deplete_oxygen_carbon = .true. ! If true, will deplete oxygen and carbon
a_disk_iter_params%deplete_oxygen_carbon_method = 'vscale' ! How to deplete oxygen and carbon
a_disk_iter_params%deplete_oxygen_method = 'tanh'
a_disk_iter_params%deplete_carbon_method = 'tanh'
a_disk_iter_params%tanh_OC_enhance_max = 1D3 ! Oxygen and carbon might also be enhanced, by at most this factor
a_disk_iter_params%gval_O = 1D-2 ! Smallest oxygen depletion factor
a_disk_iter_params%tanh_r_O = 15D0 ! Transitional radius of the depletion; in AU
a_disk_iter_params%tanh_scale_O = 3D0 ! Radius scale of the gradual transitional region
a_disk_iter_params%tanh_minval_O = 0.6D0 ! Minimum scale height of oxygen relative to the gas scale height
a_disk_iter_params%tanh_maxval_O = 0.9D0 ! Maximum ...
a_disk_iter_params%gval_C = 1D-2
a_disk_iter_params%tanh_r_C = 60D0
a_disk_iter_params%tanh_scale_C = 5D0
a_disk_iter_params%tanh_minval_C = 0.2D0
a_disk_iter_params%tanh_maxval_C = 0.7D0
!
a_disk_iter_params%do_vertical_every = 1 ! How often do we recalculate the vertical structure (if the whole calculation iterates many times)
a_disk_iter_params%nVertIterTdust = 16 ! Maximum number of iteration for dust Monte Carlo radiative transfer
a_disk_iter_params%rtol_abun = 0.2D0 ! Tolerance for checking the convergency of a cell; only when doing chemical iterations
a_disk_iter_params%atol_abun = 1D-12
a_disk_iter_params%converged_cell_percentage_stop = 0.95 ! Stop if this fraction of cells have converged.
a_disk_iter_params%n_gas_thrsh_noTEvol = 1D15 ! Grid cells with density higher than this value will simply take the dust temperature as the gas temperature; in cm-3
a_disk_iter_params%filename_list_check_refine = 'species_check_refine.dat' ! Do grid cell refinement based on species in this file.
a_disk_iter_params%threshold_ratio_refine = 10D0 ! Do refinement if the gradient (ratio) is so large
a_disk_iter_params%nMax_refine = 100 ! Max times of refinments
a_disk_iter_params%redo_montecarlo = .true. ! Redo Monte Carlo after each full chemcial run, which will recalculate the dust temperatures, UV fields, ...
a_disk_iter_params%flag_save_rates = .false. ! Whether save the calculated rates.
!
a_disk_iter_params%do_continuum_transfer = .false. ! Related to raytracing_configure
a_disk_iter_params%do_line_transfer = .false.
!
a_disk_iter_params%backup_src = .true. ! If true, it will backup files using the command backup_src_cmd
a_disk_iter_params%backup_src_cmd = 'find src/*.f90 src/*.f src/makefile inp/*dat inp/*opti | cpio -pdm '
!
a_disk_iter_params%dump_common_dir = './tmp_data_dump/' ! Common folder for backing up binary data
a_disk_iter_params%dump_sub_dir_out = 'current_model_name/' ! Subfolder in the common folder for the current model
a_disk_iter_params%iter_files_dir = 'common_results_folder/current_model_name/' ! For saving all the model data (except for the binary files)
/
! Write any notes belowAfter the thermo-chemical calculations are done, replace the
iteration_configure section of the previous configuration file with the
following, then rerun the model to do radiative transfer and make images. It
will load the data (saved in binary format) generated by the previous step.
Here we are doing radiative transfer for C18O, and assume the
raytracing_configure section of the previous configuration file is already
correctly set for this, otherwise that section needs to be modified
accordingly.
&iteration_configure
a_disk_iter_params%n_iter = 1 ! Number of iterations
a_disk_iter_params%nlocal_iter = 4 ! For numerical stability
a_disk_iter_params%do_vertical_struct = .false. ! Whether do the vertical structure calculation
a_disk_iter_params%do_vertical_with_Tdust = .true. ! Whether to use dust temperature for vertical structure calculation
a_disk_iter_params%calc_Av_toStar_from_Ncol = .false. ! Whether to calculate Av by the column density from each location towards the star
a_disk_iter_params%calc_zetaXray_from_Ncol = .false. ! Whether to calculate X-ray ionization rate based on the column density from each location towards the star
!
a_disk_iter_params%rescale_ngas_2_rhodust = .true. ! If true, the gas density is a simple scaling of the dust density
a_disk_iter_params%dust2gas_mass_ratio_deflt = 1.0D-2 ! Dust-to-gas mass ratio used for calculating the gas density from the dust density using simple scaling
a_disk_iter_params%max_num_of_cells = 10000 ! Maximum number of grid cells
!
a_disk_iter_params%deplete_oxygen_carbon = .true. ! If true, will deplete oxygen and carbon
a_disk_iter_params%deplete_oxygen_carbon_method = 'vscale' ! How to deplete oxygen and carbon
a_disk_iter_params%deplete_oxygen_method = 'tanh'
a_disk_iter_params%deplete_carbon_method = 'tanh'
a_disk_iter_params%tanh_OC_enhance_max = 1D3 ! Oxygen and carbon might also be enhanced, by at most this factor
a_disk_iter_params%gval_O = 1D-2 ! Smallest oxygen depletion factor
a_disk_iter_params%tanh_r_O = 15D0 ! Transitional radius of the depletion; in AU
a_disk_iter_params%tanh_scale_O = 3D0 ! Radius scale of the gradual transitional region
a_disk_iter_params%tanh_minval_O = 0.6D0 ! Minimum scale height of oxygen relative to the gas scale height
a_disk_iter_params%tanh_maxval_O = 0.9D0 ! Maximum ...
a_disk_iter_params%gval_C = 1D-2
a_disk_iter_params%tanh_r_C = 60D0
a_disk_iter_params%tanh_scale_C = 5D0
a_disk_iter_params%tanh_minval_C = 0.2D0
a_disk_iter_params%tanh_maxval_C = 0.7D0
!
a_disk_iter_params%do_vertical_every = 1 ! How often do we recalculate the vertical structure (if the whole calculation iterates many times)
a_disk_iter_params%nVertIterTdust = 16 ! Maximum number of iteration for dust Monte Carlo radiative transfer
a_disk_iter_params%rtol_abun = 0.2D0 ! Tolerance for checking the convergency of a cell; only when doing chemical iterations
a_disk_iter_params%atol_abun = 1D-12
a_disk_iter_params%converged_cell_percentage_stop = 0.95 ! Stop if this fraction of cells have converged.
a_disk_iter_params%n_gas_thrsh_noTEvol = 1D15 ! Grid cells with density higher than this value will simply take the dust temperature as the gas temperature; in cm-3
a_disk_iter_params%filename_list_check_refine = 'species_check_refine.dat' ! Do grid cell refinement based on species in this file.
a_disk_iter_params%threshold_ratio_refine = 10D0 ! Do refinement if the gradient (ratio) is so large
a_disk_iter_params%nMax_refine = -1 ! Max times of refinments
a_disk_iter_params%redo_montecarlo = .true. ! Redo Monte Carlo after each full chemcial run, which will recalculate the dust temperatures, UV fields, ...
a_disk_iter_params%flag_save_rates = .false. ! Whether save the calculated rates.
!
a_disk_iter_params%do_continuum_transfer = .false. ! Related to raytracing_configure
a_disk_iter_params%do_line_transfer = .true.
!
a_disk_iter_params%backup_src = .false. ! If true, it will backup files using the command backup_src_cmd
a_disk_iter_params%backup_src_cmd = 'find src/*.f90 src/*.f src/makefile inp/*dat inp/*opti | cpio -pdm '
!
a_disk_iter_params%dump_filename_chemical = 'chemical_data_iter_0001.bin' ! Chemical abundances obtained from the model calculation
a_disk_iter_params%dump_filename_physical_aux = 'physical_data_aux_iter_0001.bin' ! Physical parameters obtained from the model calculation
a_disk_iter_params%dump_filename_grid = 'grid_data_iter_0001.bin' ! Grid parameters obtained from the model calculation
a_disk_iter_params%dump_filename_physical = 'physical_data_iter_0001.bin'
a_disk_iter_params%dump_filename_optical = 'optical_data_iter_0001.bin'
a_disk_iter_params%use_backup_chemical_data = .true.
a_disk_iter_params%use_backup_grid_data = .true.
a_disk_iter_params%use_backup_optical_data = .true.
a_disk_iter_params%dump_sub_dir_in = 'current_model_name/'
!
a_disk_iter_params%dump_common_dir = './tmp_data_dump/' ! Common folder for backing up binary data
a_disk_iter_params%dump_sub_dir_out = 'current_model_name/' ! Subfolder in the common folder for the current model
a_disk_iter_params%iter_files_dir = 'common_results_folder/current_model_name/C18O/' ! If you are modeling C18O; all the images will be saved under C18O/images/
/def load_data_as_dic(filepath, comments='!', returnOriginalKeys=False):
import numpy as np
data = np.loadtxt(filepath, comments=comments)
ftmp = open(filepath, 'r')
str_comment = ftmp.readline()[1:].split()
ftmp.close()
dic = {}
for i in xrange(len(str_comment)):
dic.update({str_comment[i]: data[:, i]})
del data
if returnOriginalKeys:
return str_comment, dic
else:
return dic