I would like to use the fix bond/react command to construct a molecular model. However, I am currently confused about how to implement it correctly for my specific system. I would greatly appreciate any guidance or suggestions you could provide.
Below is a description of my model:
I want to construct a linear polymer (LJ unit, FENE model, no angle) using fix bond/react. To simplify the system, I initially pack many short molecules of the form type 2–1–1 into the simulation box. My goal is to use fix bond/react during the simulation to form a linear polymer, where type 2 beads form the main chain and type 1 beads act as side chains.
The intended structure looks like this:
2–2–2–2–2–2–2–2–2
| | | | | | | | |
1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1
I’m not sure how to properly define the templates and reactions for this process in fix bond/react, and would greatly appreciate any advice or example input files that could help.
Thank you for your suggestions. I think I’d like to approach this by organizing it into five steps. From monomer to dimer, trimer, tetramer, and eventually extended chains. Thank you once again for your helpful suggestion.
I have constructed the template file and successfully achieved step-by-step polymerization — from monomer to dimer, and from dimer to trimer. However, I am now puzzled about how to simulate radical polymerization more realistically. In radical polymerization, chain growth can occur in a stochastic manner, where, for example, a dimer can react with a trimer, or two trimers can couple. But in fix bond/react, the polymerization proceeds strictly step by step according to predefined templates. How can I simulate such random reactions occurring simultaneously?
I think each of those would be considered a different reaction and need it’s own template (until you’ve reached the necessary size of the templates / “edge”).
E.g.
Reaction 1: 2 Monomers → Dimer
Reaction 2: Monomer + Dimer → Trimer
Reaction 3: Monomer + Trimer
Reaction 4: 2 Dimers
Reaction 5: Dimer + Trimer
Reaction 6: 2 Trimers
I think after that growth should continue with these reactions as you only specify bonds and angles. And the rest can be behind the “edge” particles.
I am not sure if the sequence of the reaction definitions play a role role here. You could play around with the probability parameter, so that not all reactions happen instantly, but the system has time to evolve.
as @wolfgang mentioned, ‘edge atoms’ are atoms that connect to connect to the rest of a polymer chain (or other larger molecule). All of the examples shipped with LAMMPS involve polymerization and include edge atoms, so those could be a good place to start.
