Generate charge exchange reactions

When you run ProDiMo with the flag

.true.     ! check_network

a number of consistency checks about the chemical network will be executed. Among those checks, ProDiMo will generate missing charge exchange reactions between molecules, PAHs and dust grains, and proton exchange reactions between molecules. If you want to run models with charging states of dust grains, this flag is mandatory, because we need to generate the reactions that exchange charges between dust grains and molecular ions (see Dust charge chemistry).

Charge exchange and proton exchange reactions are quite simple and usually barrier-free. Therefore, we believe that completeness is more important here than accurate rates. Charges and protons should be passed freely among molecules, based on reaction enthalpy. In general, if a reaction is exothermal (i.e. heat is released dHf < 0), that reaction should be possible and barrier-free, and the rate coefficient should be close to the Langevin rate which is temperature-independent. To determine dHf, we use the heat of formation data at 0K from ~/ProDiMo/data/ChemicalNetwork/Heat_of_formation.dat

This principle is applied to the automatic generation of reactions in ProDiMo, which are then stored in file Reactions_extra.in.csv. ProDiMo will then stop and ask the user whether they agree to add these reactions by typing

cat Reactions_extra.in.csv >> Reactions.in.csv

Please note, if your model directory does not include the Reactions.in.csv file, copy the file data/ChemicalNetwork/Reactions.in.csv to your model directory, and execute the command above. It might be necessary to repeat this step (i.e. check again for the Reactions_extra.in.csv). Once ProDiMo is satisfied it will properly run the full model even if check_network=True.

The creation of extra reactions is controlled by the following flags

.true.      ! auto_charge_exchange   
.false.     ! auto_grain_endotherm    
.false.     ! auto_proton_exchange     
5000.0      ! auto_create_barrier

with their default values listed above. That means that

  • charge exchange reactions (between molecules, PAHs, dust) are generated
  • the energy barrier for endotherm reactions to be generated is 5000K (although that is only applied to reactions between molecules and PAHs)
  • endotherm charge exchange reactions involving dust grains are NOT generated
  • proton exchange reactions (between molecules) are NOT generated.

Changing these parameters will have the following effect

  1. auto_charge_exchange=F only creates the necessary dust charge exchange reactions, but not those among molecules and PAHs
  2. auto_grain_endotherm=T also creates endotherm dust charge exchange reactions
  3. auto_proton_exchange=T also creates proton exchange reactions between molecules, including the endotherm ones.
  4. with auto_create_barrier=0 one can suppress the generation of any endotherm reactions

If endotherm reactions are generated, the third reaction parameter C in the modified Arrhenius law is put to C = Max{dHf/k,0} where k is the Boltzmann constant. For endotherm reactions to be generated, dHf/k < auto_create_barrier (the value of the parameter ! auto_create_barrier) must hold.