Configuration

The full 0-liquid-styrene.yaml is short — no reactions, no CURE, no postcure. It is just enough to parameterize a single monomer, build a low-density box, and run the densification + anneal cascade.

# htpolynet -- Example 0 -- Liquid Styrene
#
# Self-contained config: the styrene monomer is generated from SMILES
# (RDKit path via the atom-mapping syntax).  Run with:
#
#   htpolynet run -diag diagnostics.log 0-liquid-styrene.yaml
#
# This example produces a densified liquid of "active" styrene monomers
# (no curing).  After the run completes you can compute properties with
# `htpolynet analyze` -- save the following as `ck.yaml` and invoke
# `htpolynet analyze -cfg ck.yaml -ocfg 0-liquid-styrene.yaml -proj proj-0`:
#
#   - command: check
#     subdir: analyze/check
#     links: [systems/densification/densified-npt.trr]
#     options: {f: densified-npt.trr}
#     outfile: check.out
#     matchlines: ['Last frame', 'Coords']
#   - command: report-methods
#     subdir: analyze/report-methods
#     links: [systems/densification/densified-npt.tpr]
#     options: {s: densified-npt.tpr, m: report.tex}
#   - command: freevolume
#     subdir: analyze/freevolume
#     links:
#       - systems/densification/densified-npt.tpr
#       - systems/densification/densified-npt.trr
#     options: {s: densified-npt.tpr, f: densified-npt.trr}
#
# Cameron F. Abrams -- cfa22@drexel.edu

Title: Liquid of Active Styrene Monomers
gromacs:
  gmx: gmx
  gmx_options: -quiet -nobackup
  mdrun: gmx mdrun
  mdrun_options:
    gpu_id: 0            # auto-stripped at runtime if gmx is not GPU-capable or no GPU is visible
ambertools:
  charge_method: gas
constituents:
  STY:
    smiles: "c1ccccc1[CH2:1][CH3:2]"
    reactive_atoms: {1: C1, 2: C2}
    count: 1000
densification:
  initial_density: 300.0  # kg/m3
  equilibration:
    - ensemble: min
    - ensemble: nvt
      temperature: 300.0
      ps: 10.0
    - ensemble: npt
      temperature: 300.0
      pressure: 10.0
      ps: 200.0
precure:
  preequilibration:
    ensemble: npt
    temperature: 300        # K
    pressure: 1.0           # bar
    ps: 200
  anneal:
    ncycles: 2
    initial_temperature: 300.0
    cycle_segments:
      - T: 300.0
        ps: 0
      - T: 600.0
        ps: 20
      - T: 600.0
        ps: 20
      - T: 300.0
        ps: 20
      - T: 300.0
        ps: 20
  postequilibration:
    ensemble: npt
    temperature: 300.0      # K
    pressure: 1.0           # bar
    ps: 100

A block-by-block walk-through:

Title

A free-text label for the run; appears in logs and in the title field of generated topology/structure files.

gromacs

Tells htpolynet how to invoke GROMACS. gmx_options are passed to every gmx invocation; mdrun_options are passed to mdrun only. The gpu_id: 0 line is left in by default and the runtime will automatically strip it (with a warning) if the gmx build is not GPU-capable or no GPU is visible.

ambertools

Selects the partial-charge method for antechamber; gas is Gasteiger and is fast and good enough for a non-reactive densification.

constituents

Declares the molecular species in the box. Here, one species (STY, 1000 copies) generated from SMILES. See monomer for the atom-mapping details.

densification

The post-pack equilibration cascade. Starts at initial_density: 300 kg/m³ (deliberately loose so the pack succeeds without overlaps) and runs minimization → 10 ps NVT at 300 K → 200 ps NPT at 300 K, 10 bar. The deliberately high pressure accelerates compaction.

precure

Despite the name, precure is not chemically a curing step — it is the post-densification equilibration that htpolynet runs whether or not a cure is configured. Here it is:

• preequilibration — 200 ps NPT at 300 K, 1 bar (relax the pressure jolt from densification);

• anneal — two 300 K → 600 K → 300 K cycles, 80 ps per cycle, useful for shaking the liquid out of any pack-induced local traps;

• postequilibration — 100 ps NPT at 300 K, 1 bar.

The comment block at the top of the YAML also sketches an htpolynet analyze configuration (ck.yaml) you can run after the build to compute free volume and similar properties; see results and the Post-build simulations and analyses section.