The Configuration File

We previously described an example configuration file for making a system of polystyrene, where all the directives were explained in detail. Here we will only highlight excerpts from pMSTY.yaml.

Constituents Directives

We’ll use a very small system of only 127 monomers.

constituents:
  EMB:
    count: 127

Reactions Directives

We need only define the polymerization reaction that links two monomers and the capping reaction that “unactivates” any unreacted monomers.

reactions:
  - name:        emb1_1
    stage:       cure
    reactants:
      1: EMB
      2: EMB
    product:     EMB~C1-C2~EMB
    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
  - name:         embCC
    stage:        cap
    reactants:
      1: EMB
    product:      EMBCC
    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

With the configuration file specified, let’s watch what happens when we run HTPolyNet to make the build.