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.