Fix bond/react

I am using fix bond/react command of lammps for cross-linking. It worked excellent when I cross-linked the polymer only. Now, I am having a system comprised of nanotube and polymer. I want to keep my nanotube fixed (not moving in any direction). So, I have grouped nanotube as NT and polymer as poly. Now, I am using the fix bond/react command like:

fix myrxns poly bond/react stabilization yes statted_grp 0.03 react myrxn1 poly 1 0 3.25 mol1 mol2 rxn1_map

Here, I am unsure if I time integrate the statted_grp created during fix bond/react, whether the statted_grp created here will involve only the atoms of polymer that were not taking part in the reaction or it will involve all the atoms (poly and NT) that wre not taking part.

Thanks for your reply in advance.

From the documentation:

Fix bond/react creates and maintains two important dynamic groups of atoms when using the stabilization keyword. The first group contains all atoms currently involved in a reaction; this group is automatically thermostatted by an internally-created nve/limit integrator. The second group contains all atoms currently not involved in a reaction. This group should be used by a thermostat in order to time integrate the system. The name of this group of non-reacting atoms is created by appending ‘_REACT’ to the group-ID argument of the stabilization keyword, as shown in the second example above.

Sorry but my doubt is something different. My system is having nanotube and polymer monomers. Now, I cross-linked polymer monomers only (bonds are creating between unreacted polymer monomers). So for that, I group them as NT(for nanotubes) and poly (for polymers). Then, I used fix bond/react as:

fix myrxns poly bond/react stabilization yes statted_grp 0.03 react myrxn1 poly 1 0 3.25 mol1 mol2 rxn1_map

Now, if suppose my system is having 100 polymer atoms and 100 nanotubes atoms and 10 took part in reactions then, is the statted_grp will contains the remaining 90 atoms of polymers (that are not taking part in the reaction) or it contain atoms of 100 nanotubes and remaining 90 atoms?

As from the documentation, it is not clear which all atoms the statted_grp will have (only the remaining atoms of polymer or the remaining atoms of polymers and nanotube both).

Kindly, clear me please.

This is something that you can very easily confirm yourself without any additional explanations. Just use the write_dump command to write out a custom dump file for the atoms of just that group with the information of that atom IDs (and types and other info if desired).

Thank you so much axel sir. You are really great.
Your explanation always helps me.

In your example, you can define a thermostat for the polymer atoms that are not reacting using the group ‘statted_grp_REACT’ (which is created internally by fix bond/react). The nanotube atoms will not be included

Thank you so much sir.