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Bead-Spring (Coarse-Grained)

BeadSpringPolymer builds coarse-grained bead-spring polymer models — Kremer–Grest-style chains of Lennard-Jones beads — and writes LAMMPS data files directly, with no SMILES, no atom typing, and no moltemplate. Use it for large systems, long chains, and polymer physics studies where chemical detail is not the point.

from AutoPoly import System, BeadSpringPolymer, BeadType

system = System(out="cg_melt")

bsp = BeadSpringPolymer(
    name="homopolymer",
    system=system,
    n_chains=50,
    bead_types=[BeadType(name="A", mass=1.0, epsilon=1.0, sigma=1.0)],
    sequence=[("A", 100)],        # 100 beads of type A per chain
    topology="linear",
    bond_style="harmonic",
    pair_style="lj",
    generation_method="saw",
)
bsp.generate_data_file()

Building blocks

Class Purpose
BeadType One bead species: name, mass, LJ epsilon and sigma
AngleType Bending stiffness for a bead triplet (k, theta0)
SAWConfig Tuning for self-avoiding-walk generation (trials, backtracking, ring closure)
MCConfig Tuning for Monte Carlo pre-equilibration (moves, temperature, steps)

Sequences and topologies

The sequence describes one chain and accepts several forms:

sequence=[("A", 100)]              # homopolymer: 100 × A
sequence=[("A", 50), ("B", 50)]    # diblock: A₅₀-b-B₅₀
sequence="AABB"                    # shorthand by bead name
sequence=["A", "A", "B", "B"]      # explicit per-bead list

Topologies:

  • "linear" — chain with two free ends
  • "ring" — cyclic chain; the generator spends extra trials closing the ring (SAWConfig.ring_closure_trials, ring_closure_tolerance)

Potentials

  • Bonds — "harmonic" (E = K(r−r₀)²) or "fene" (finitely extensible nonlinear elastic, the standard for bead-spring melts)
  • Pairs — "lj" (full Lennard-Jones, cutoff 2.5σ) or "wca" (repulsive Weeks–Chandler–Andersen, cutoff ≈ 1.122σ)
  • Angles — optional per-triplet stiffness via AngleType

Generation methods

generation_method Speed Result
"geometric" Fastest Simple geometric placement; may contain overlaps
"saw" (default) Fast Self-avoiding walk — overlap-free coils
"mc" Slow Monte Carlo pre-equilibration (MCConfig) — relaxed starting configurations

The SAW generator shares its collision detector with the atomistic MC placement engine; box size comes from the target bead density (default 0.85 beads/σ³).

Output

generate_data_file() writes a complete LAMMPS data file (masses, pair/bond/angle coefficients, atoms, bonds, angles) under <System out>/<name>/ — no system.in.* split files, since everything is self-contained in reduced units.

See also