The Configuration File

The complete 1-polystyrene.yaml carried by the depot:

# htpolynet -- Example 1 -- Polystyrene
#
# Self-contained config: the styrene monomer is generated from SMILES by
# htpolynet itself.  The two reactive vinyl carbons are identified inline in
# the SMILES with atom-map labels [CH2:1] and [CH:2]; the `reactive_atoms`
# block maps those labels to the atom names (C1, C2) referenced by the
# reactions below.  This path requires RDKit (`pip install 'htpolynet[smiles]'`,
# or use the container which ships RDKit).
#
#   htpolynet run -diag diagnostics.log 1-polystyrene.yaml
#
# Cameron F. Abrams -- cfa22@drexel.edu

Title: polystyrene
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
      ps: 10
    - ensemble: npt
      temperature: 300
      pressure: 10
      ps: 200
precure:
  preequilibration:
    ensemble: npt
    temperature: 300        # K
    pressure: 1             # bar
    ps: 200
  anneal:
    ncycles: 2
    initial_temperature: 300
    cycle_segments:
      - T: 300
        ps: 0
      - T: 600
        ps: 20
      - T: 600
        ps: 20
      - T: 300
        ps: 20
      - T: 300
        ps: 20
  postequilibration:
    ensemble: npt
    temperature: 300        # K
    pressure: 1             # bar
    ps: 100
CURE:
  controls:
    search_radius: 0.5  # nm
    radial_increment: 0.25      # nm
    max_iterations: 150
    desired_conversion: 0.95
    late_threshold: 0.85
  drag:
    trigger_distance: 0.6   # nm
    increment: 0.08         # nm
    limit: 0.3              # nm
    equilibration:
      - ensemble: min
      - ensemble: nvt
        temperature: 600
        nsteps: 1000
      - ensemble: npt
        temperature: 600
        pressure: 1
        nsteps: 2000
  relax:
    increment: 0.08         # nm
    equilibration:
      - ensemble: min
      - ensemble: nvt
        temperature: 600
        nsteps: 1000
      - ensemble: npt
        temperature: 600
        pressure: 1
        nsteps: 2000
  equilibrate:
    ensemble: npt
    temperature: 300       # K
    pressure: 1            # bar
    ps: 100
  gromacs:
    rdefault: 0.9          # nm
postcure:
  anneal:
    ncycles: 2
    initial_temperature: 300
    cycle_segments:
      - T: 300
        ps: 0
      - T: 600
        ps: 20
      - T: 600
        ps: 20
      - T: 300
        ps: 20
      - T: 300
        ps: 20
  postequilibration:
    ensemble: npt
    temperature: 300       # K
    pressure: 1            # bar
    ps: 100
reactions:
  - name:        sty1_1
    stage:       cure
    reactants:
      1: STY
      2: STY
    product:     STY~C1-C2~STY
    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:         styCC
    stage:        cap
    reactants:
      1: STY
    product:      STYCC
    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

A block-by-block walk-through (skipping the blocks already covered in example 0 — Title, gromacs, ambertools, densification, precure):

constituents

One species: STY, 1000 copies, generated from SMILES. See monomer for the atom-mapping details.

CURE

Controls the Connect-Update-Relax-Equilibrate cycle:

• controls.search_radius (0.5 nm) and controls.radial_increment (0.25 nm) set the starting search radius for finding reactive pairs and how aggressively to grow it when nothing is found.

• controls.max_iterations caps the number of CURE iterations even if conversion has not yet been reached.

• controls.desired_conversion (0.95) is the target. Conversion is defined relative to the maximum possible bonds for the system.

• controls.late_threshold (0.85) is the conversion above which htpolynet stops applying the per-reaction probability filter — once you are close to saturation, every eligible bond is worth taking.

• drag configures the optional preupdate dragging step that pulls almost-eligible pairs together before bond formation. With trigger_distance: 0.6 nm, increment: 0.08 nm, and limit: 0.3 nm, htpolynet will progressively shorten candidate bond distances by adding a restraint and running short MD between increments.

• relax configures the bond-relaxation step that runs after every CURE topology update — minimization plus a 1 ps NVT at 600 K plus a 2 ps NPT at 600 K / 1 bar.

• equilibrate runs a 100 ps NPT at 300 K / 1 bar at the end of each iteration.

• gromacs.rdefault (0.9 nm) is the nonbonded cutoff used for CURE-stage MD runs.

Tip

The CURE.controls.min_bonds_per_iteration knob (default 10) sets the minimum number of bonds an iteration must find before it stops growing the search radius. Bigger values batch more bonds per iteration and so run fewer relax/equilibrate cycles overall, at the cost of more strained bonds in each batch. htpolynet automatically clamps the effective floor against how many bonds are still possible, so demanding min_bonds_per_iteration: 50 near end-of-cure won’t stall the build. Empirically, 10 is a good operating point for the epoxy/amine examples in this tutorial set: see Running the Build for the measured iteration counts on DGEBA/PACM.

postcure

The post-cure equilibration cascade: two more 300/600 K annealing cycles followed by a 100 ps NPT at 300 K / 1 bar.

reactions

The cure and cap reactions described on the previous page.