Post-build simulations and analyses¶

DFA/FDE is a cross-linked epoxy thermoset with the same overall reaction mechanism as example 3, so the same postsim and analyze suite applies: annealing and equilibration, a temperature ladder for T_g, uniaxial deformations for E, and a free-volume measurement.

The DGEBA-PACM Epoxy Thermoset walks through each stage in detail with representative production plots; this section follows the same pattern.

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
- deform:
    input_top: systems/final-results/final.top
    input_gro: postsim/equilibrate/equilibrate.gro
    subdir: postsim/deform-x
    T: 300
    P: 1
    direction: x
    edot: 0.001
    ps: 10
- deform:
    input_top: systems/final-results/final.top
    input_gro: postsim/equilibrate/equilibrate.gro
    subdir: postsim/deform-y
    T: 300
    P: 1
    direction: y
    edot: 0.001
    ps: 10
- deform:
    input_top: systems/final-results/final.top
    input_gro: postsim/equilibrate/equilibrate.gro
    subdir: postsim/deform-z
    T: 300
    P: 1
    direction: z
    edot: 0.001
    ps: 10

Run it:

$ htpolynet postsim -cfg postsim.yaml -ocfg 4-dfda-fde-epoxy-thermoset.yaml -proj proj-0

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, and comment on densification and equilibration adequacy.

Glass-transition temperature and Young’s modulus¶

After postsim finishes, fit T_g and E with:

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

This emits tg.png, e.png, E.csv, and per-ladder CSVs in proj-0/plots/.

Placeholder

TODO: insert proj-0/plots/tg.png and proj-0/plots/e.png here, report the heating/cooling T_g values and E (in GPa), and contrast with the DGEBA/PACM numbers in DGEBA-PACM Epoxy Thermoset to highlight how chemistry choice shifts thermomechanical properties.

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.