Reactions

Cure reaction

The only inter-monomer reaction is the bond between C1 of one styrene and C2 of another:

reactions:
  - name:        sty1_1
    stage:       cure
    reactants:
      1: STY
      2: STY
    product:     STY~C1-C2~STY
    probability: 1.0
    atoms:
      A:
        reactant: 1
        resid: 1
        atom: C1
        z: 1
      B:
        reactant: 2
        resid: 1
        atom: C2
        z: 1
    bonds:
      - atoms: [A, B]
        order: 1

The product name STY~C1-C2~STY is used internally by htpolynet to build and parameterize the dimer template. This template provides atom types, charges, and bonded interactions that are mapped back onto the growing polymer whenever a new C1–C2 bond is formed.

Chain expansion

Because styrene polymerizes by C=C double-bond opening, the reactive atoms C1 and C2 can form chains of arbitrary length through the polymer backbone. htpolynet automatically expands the base reaction above into all combinations needed to correctly parameterize trimer and tetramer templates. These cover the full set of dihedral topologies that arise as chains grow. You do not need to list these explicitly; htpolynet reports them in the console log at the start of a run.

Cap reaction

Once CURE finishes, any monomer that did not react still carries its two sacrificial hydrogens and its C1–C2 atoms remain in the “active” (saturated) form. The cap reaction converts these back to the true C=C double bond:

- name:         styCC
  stage:        cap
  reactants:
    1: STY
  product:      STYCC
  probability:  1.0
  atoms:
    A:
      reactant: 1
      resid: 1
      atom: C1
      z: 1
    B:
      reactant: 1
      resid: 1
      atom: C2
      z: 1
  bonds:
    - atoms: [A, B]
      order: 2

The stage: cap label means this reaction is applied only after CURE has completed.

The next thing we consider is the configuration file.