Post-build simulations and analyses¶

Polystyrene is a linear polymer rather than a cross-linked network, so a uniaxial-deformation measurement of Young’s modulus is not particularly meaningful for the short chains built here. What we can do is anneal and equilibrate the system, then perform a temperature ladder to estimate the glass-transition temperature, and use analyze to measure the fractional free volume of the equilibrated melt.

The DGEBA-PACM Epoxy Thermoset walks through the full set of postsim and analyze techniques in detail (including deformation, which is well-suited to thermosets); this section adapts that workflow to a linear polymer.

The postsim configuration¶

Create postsim.yaml in the project base directory:

- anneal:
    input_top: systems/final-results/final.top
    input_gro: systems/final-results/final.gro
    P: 1
    T0: 300
    T1: 600
    ncycles: 2
    T0_to_T1_ps: 10
    T1_ps: 10
    T1_to_T0_ps: 10
    T0_ps: 10
- equilibrate:
    input_top: systems/final-results/final.top
    input_gro: postsim/anneal/anneal.gro
    T: 300
    ps: 100
- ladder:
    input_top: systems/final-results/final.top
    input_gro: postsim/equilibrate/equilibrate.gro
    subdir: postsim/ladder-heat
    Tlo: 300
    Thi: 600
    deltaT: 5
    ps_per_rise: 10
    ps_per_run: 90
    warmup_ps: 10
- ladder:
    input_top: systems/final-results/final.top
    input_gro: postsim/ladder-heat/ladder.gro
    subdir: postsim/ladder-cool
    Tlo: 300
    Thi: 600
    deltaT: -5
    ps_per_rise: 10
    ps_per_run: 90
    warmup_ps: 10

Run it:

$ htpolynet postsim -cfg postsim.yaml -ocfg 1-polystyrene.yaml -proj proj-0

This produces proj-0/postsim/{anneal,equilibrate,ladder-heat,ladder-cool}/ with the usual Gromacs outputs plus on-the-fly density-vs-time plots.

Density during annealing and equilibration¶

Placeholder

TODO: insert the rho_v_ns.png plots from proj-0/postsim/anneal/ and proj-0/postsim/equilibrate/ here. Note whether the annealing has actually densified the system (it usually fails to in builds this short) and whether the post-anneal equilibration trace is flat over the second half.

Glass-transition temperature¶

After postsim has produced the heating and cooling ladders, fit T_g from the density-vs-temperature traces with:

$ htpolynet plots post --cfg postsim.yaml --proj proj-0

This emits tg.png plus per-ladder CSVs in proj-0/plots/.

Placeholder

TODO: insert proj-0/plots/tg.png and report the heating and cooling T_g values from the console output here. In simulations this short, expect significant heating/cooling hysteresis — comment on what production-length runs would be needed to get a converged estimate.

Free volume¶

Use htpolynet analyze to invoke gmx freevolume on the equilibration trajectory. Create fv.yaml:

- command: freevolume

Then:

$ htpolynet analyze -cfg fv.yaml -proj proj-0

Placeholder

TODO: report the fractional free volume (and standard error) from proj-0/analyze/freevolume/ffv.dat here. Glassy polystyrene at 300 K typically has FFV in the 0.15–0.20 range.