Conditions for the occurrence of reactions in bond/react

Hi there,

I’m having some problems with conditions for the occurrence of reactions in the fix bond/react command. Any help on the issues would be greatly appreciated!

The following is described in the official manual,https://docs.lammps.org/fix_bond_react.html

Three physical conditions must be met for a reaction to occur. First, an initiator atom pair must be identified within the reaction distance cutoffs.
Second, the topology surrounding the initiator atom pair must match the topology of the pre-reaction template. Only atom types and bond connectivity are used to identify a valid reaction site (not bond types, etc.). Finally, any reaction constraints listed in the map file (see below) must be satisfied. If all of these conditions are met, the reaction site is eligible to be modified to match the post-reaction template.

I don’t quite understand what bond connectivity refers to here. As shown below, I want the atom T15 I89-1 and atom T16 I125-2 to be bonded. To achieve this, I included as many atoms as possible in the pre-reaction template (17 atoms, including three bonds around atom T16 I125-2). However, the reaction is not triggered.

17 atoms

Next, I tried including different numbers of atoms in the pre-reaction template, as shown below,
11 atoms 23 atoms

When the pre-reaction template contains 11 atoms and 23 atoms, as shown above, the reaction will not be triggered.

5 atoms

Finally, the reaction was triggered correctly when there were only 5 atoms. I am now confused as to how many atoms need to be included in the pre-react template.

Second, the topology surrounding the initiator atom pair must match the topology of the pre-reaction template. Only atom types and bond connectivity are used to identify a valid reaction site (not bond types, etc.).

I don’t know if this understanding is correct: the conformation of molecules changes too much during the high-temperature relaxation process, such as carbon chain curling or flipping. Therefore, the pre_template must contain as few atoms as possible.

Anyway, thank you all so much for your time and help.

Zilin

Bond connectivity refers to the bonds defined in your simulation (in other words, which atoms are directly connected to each other). Valid reaction sites are determined only by looking at the atom types and which atoms they are connected to (not more complicated things such as bond types, angles, etc.).

Adding more atoms should not prevent the reaction from occuring, as long as they all have the correct atom type. You should double check that your larger reaction templates are correct, including atom types, bonds and edge atom IDs. It is difficult to say more without a simple example that reproduces the problem.