The params.dat
Important
The required config.mk, makefile, and params.dat files are provided as templates. To set up your simulation:
Copy
config.mkandmakefilefrom3D-PDR/templates/1D/or3D-PDR/templates/3D/into yoursrc/directory, based on your simulation type (1D or 3D).Copy the
params.datfile from the same template directory into the3D-PDR/home directory.
The params.dat file configures input/output settings, PDR environmental parameters, thermal balance options, coolants, and other technical parameters for 3D-PDR simulations.
Custom parameter files (e.g., paramsUser.dat) can be specified using the command-line options -p= or --params:
./3DPDR -p=paramsUser.dat
Note
Parameter filenames must not exceed 50 characters.
Input/Output - Densities
1) ics !ICs directory
2) 1Dn30.dat !ICs file
3) sims !Output directory
4) test !Output prefix
Entry 1: Directory containing initial conditions and density distributions.
Entry 2: Input file specifying the 1D density distribution.
Entry 3: Output directory where simulation results are stored.
Entry 4: Prefix for output files (e.g., results will be saved as
sims/test.pdr.fin).
PDR Parameters
5) 10 !G0 (in Draine field units) -x to +x in 1D
6) 1.0E-16 !Cosmic-ray ionization rate (s^-1)
7) 0.0 !Xray flux (erg/cm2/s)
8) 1.0 !Dust-to-gas normalized to 1e-2
9) 1.0 !Turbulent velocity (km/s)
10) 1e7 !End time (yr)
11) 1.0E-5 !Grain radius (cm)
12) 6.289e-22 !Av conversion factor
13) 3.02 !UV factor
14) 0 !Redshift (for CMB temperature)
15) 0.7 !Av critical (SUPRATHERMAL switch)
16) 3.3 !Alfven velocity (km/s) (SUPRATHERMAl switch)
Entry 5: FUV radiation field intensity normalized to Draine (1978) spectral shape.
For
DIMENSIONS = 1: one-sided radiation fieldFor
DIMENSIONS = 3: isotropic radiation field (each of 12 HEALPix rays receives intensity/12)
Entry 6: Cosmic-ray ionization rate (\({\rm s}^{-1}\)), fixed throughout the cloud.
Entry 7: X-ray flux (\(\rm erg/cm^2/s\)). Not recommended to change in this version.
Entry 8: Dust-to-gas ratio normalized to \(10^{-2}\). For non-solar metallicities, modify this value and specify elemental abundances separately.
Entry 9: Microturbulent velocity (km/s) for turbulent heating.
Entry 10: Chemical evolution end time (years). Default 10 Myr ensures chemical equilibrium; adjustable for younger cloud studies.
Entry 11: Grain radius (cm).
Entry 12: Visual extinction conversion factor from Roellig et al. (2007).
Entry 13: UV attenuation factor from Roellig et al. (2007).
Entry 14: Redshift value determining CMB temperature.
Entry 15: Critical Av for
SUPRATHERMAL = 1switch (Av threshold where suprathermal CO formation via CH⁺ becomes negligible).Entry 16: Alfvén velocity (km/s) for
SUPRATHERMAL = 1switch.
Note
Entries 15 and 16 are only used when compiled with SUPRATHERMAL = 1.
Softened-Power-Law Cosmic Ray Attenuation
For softened-power-law cosmic ray attenuation, modify the parameter structure as follows:
5) 10 !G0 (in Draine field units) -x to +x in 1D
6a) 1.0E-16 !Surface cosmic-ray ionization rate, zeta0 (s^-1)
6b) 1.0E21 !Normalizing column density, N0
6c) -1.0 !Attenuation slope, alpha
.... continued as normal
Add entries 6b and 6c as new lines in your parameter file.
Numerical Parameters
Ray-tracing, ODE Solver, and Chemistry Iterations
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Ray-tracing parameters |
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17) 0 !HEALPix level of refinement
18) 1.3 !Theta critical (0<phi<pi/2)
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ODE Solver parameters |
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19) 1.0D-8 !relative abundance tolerance
20) 1.0D-30 !absolute abundance tolerance
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Chemistry iterations |
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21) 8 !First set of Chemical Iterations
22) 6000 !Total iterations
Warning
Modify these values only if you understand their impact on numerical stability and convergence.
Thermal Balance Parameters
23) 40.0 !Gas temperature for isothermal models
24) 10.0 !Floor temperature (if <Tcmb it's set to Tcmb)
25) 30000.0 !Maximum allowed gas temperature
26) 20.0 !Dust temperature for isothermal dust models
27) 0.005 !Fcrit (% Accuracy)
28) 0.01 !Tdiff (maximum temperature difference)
Entry 23: Gas temperature for isothermal models (requires
THERMALBALANCE = 0andGUESS_TEMP = 0in makefile).Entry 24: Minimum gas temperature floor. Automatically raised to CMB temperature if lower.
Entry 25: Maximum allowed gas temperature (not recommended to change).
Entry 26: Dust temperature for isothermal dust models (requires
DUST = 0in makefile).Entry 27: Thermal balance accuracy tolerance (modify with caution).
Entry 28: Maximum temperature difference for thermal balance convergence (modify with caution).
Coolant Files
29) 12co.dat !CO Do not change the following order
30) 12c+.dat !CII
31) 12c.dat !CI
32) 16o.dat !OI
The default coolant list (12CO, C⁺, C, O) should maintain the specified order. Additional coolants can be appended after 16o.dat, though this may impact computational performance.
Adding Additional Coolants
Including additional coolants enables study of their emission lines. 3D-PDR computes level populations for all specified coolants, which can be used by RT-tool and RT-synth for radiative transfer calculations.
To add coolants beyond the defaults:
Verify the chemical network includes the desired species
Append coolant filenames to
params.datafter the default entries
Example:
29) 12co.dat !CO Do not change the following order
30) 12c+.dat !CII
31) 12c.dat !CI
32) 16o.dat !OI
33) hco+.dat !HCO⁺
34) cs.dat !CS
Custom Coolant Data Files
For coolants not available in chemfiles/, download from the LEIDEN LAMBDA database and modify the file header:
Original LEIDEN format:
!MOLECULE
O (neutral atom)
!MOLECULAR WEIGHT
16.0
!NUMBER OF ENERGY LEVELS
5
Modified for 3D-PDR:
!MOLECULE
O !Name matching species_NETWORK.d
!MOLECULAR WEIGHT
16.0
!NUMBER OF ENERGY LEVELS
5 27 !Add max "COLL TEMPS" count
Multiple coolants can be added by extending the parameter file list. Each additional coolant increases computation time.