Editing or using a different chemical network

VULCAN is developed in a flexible way, so that the chemical network is not hard coded. You can switch networks or edit the default one.

Switching networks

Edit config.py:

network = 'thermo/CHO_photo_network.txt'  # Use C, H, O only

Then run:

python vulcan.py

Do NOT use -n flag when changing networks!

Editing the default network

Network file format

Each reaction is written as:

[ Reactant1 + Reactant2 -> Product1 + Product2 ]  A  B  C

Where A, B, C are Arrhenius coefficients: \(k = A T^B \exp(-C/T)\)

Example from NCHO_photo_network.txt:

[ OH + H2 -> H2O + H ]  3.57E-16    1.520   1740.0
[ O + H2 -> OH + H   ]  8.52E-20    2.670   3160.0

Steps to edit

Open the network file:
```
nano thermo/NCHO_photo_network.txt
```
Add a reaction: Insert at appropriate location:
```
[ New_species1 + New_species2 -> Product1 + Product2 ]  A   B   C
```
where you replace A, B, C with the appropriate Arrhenius coefficients.
Remove a reaction: Delete the line
Change rate coefficients: Edit the A, B, C values
Save and run:
```
python vulcan.py
```

VULCAN will regenerate chem_funs.py with your changes.

Adding new species

If you add new species, you must add NASA-9 thermodynamic data:

Find the coefficients in thermo/NASA9/nasa9_2002_E.txt or new_nasa9.txt
Create a file in thermo/NASA9/ with the species name, e.g., MY_SPECIES.txt. The format of the NASA 9 polynomials is as follows:
```
a1 a2 a3 a4 a5
a6 a7 0. a8 a9
```

Note the "0." separator between a7 and a8!

Check thermo/all_compose.txt for your new species. If you cannot find your species, add it in the same format, e.g.:

species         H   O   C   He  N   S   P   Na  K   Si  Fe  Ar  Ti  V   Mg  Ca  e   mass    
H2O             2   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   18.016

Run VULCAN:
```
python vulcan.py
```

Important notes

Forward reactions only - List only forward reactions; VULCAN automatically computes reverse reactions from thermodynamics
Three-body reactions and photodissociation reactions - Listed separately after a comment line in default networks
Don't skip chemical regeneration - Always run WITHOUT -n after editing networks!

Remember: Editing reaction networks requires understanding the chemistry. Start with existing networks and make small changes!