The species_[network].d

To modify the initial elemental abundances in your PDR model, edit the species_NETWORK.d file located in the chemfiles/ directory. The specific file name depends on the chemical network you are using.

Important

No re-compilation of 3D-PDR is required when only modifying elemental abundances. Simply edit the appropriate species file and run your simulation.

The species_NETWORK.d file contains the initial abundance values for all chemical elements included in the network. Modify these values according to your desired metallicity or abundance pattern.

Example modification for the REDUCED network

If using the species_reduced.d network, you would edit chemfiles/species_reduced.d and adjust the abundance values for elements such as hydrogen, carbon, oxygen, etc., to reflect your desired chemical composition.

When editing species_reduced.d, pay special attention and change only the following species while leaving all the rest equal to 0.0:

  • C+ (entry 11): Carbon abundance should be specified here rather than in neutral C (entry 25) to allow the code to start the chemical network from the ionized phase of carbon

  • O (entry 30): Oxygen abundance

  • H (entry 32): Atomic hydrogen abundance

  • H2 (entry 31): Molecular hydrogen abundance

  • He (entry 26): Helium abundance

  • Mg+ (entry 10): Ionized magnesium abundance (if desired)

Locate the relevant entries in your species file and modify the abundance values (third column):

11,C+,1.40e-04,12.0    # Carbon abundance
30,O,3.00e-04,16.0     # Oxygen abundance
32,H,4.00e-01,1.0      # Atomic hydrogen
31,H2,3.00e-01,2.0     # Molecular hydrogen
26,He,1.00e-01,4.0     # Helium abundance
10,Mg+,0.0,24.0        # Ionized magnesium

Note

  • The total hydrogen abundance must satisfy: HI + 2×H₂ = 1 at all times

  • The default values (H = 0.4, H₂ = 0.3) satisfy this constraint: 0.4 + 2×0.3 = 1

  • Electron abundance (e-, entry 33) is automatically calculated by 3D-PDR from the input ionized elements and should not be modified manually, unless specialized runs need to be performed

  • For specialized runs, you may adjust the HI/H₂ ratio, but always maintain the total hydrogen constraint

After saving your changes to the species file, 3D-PDR will automatically use the updated abundances in your next simulation without requiring recompilation.