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The 3-Step Workflow

AutoPoly turns SMILES strings into LAMMPS input files through a small, fixed set of objects. Every script — from a single solvent box to a multi-block copolymer melt — follows the same three steps.

System  →  Polymer / Molecule  →  generate  →  LAMMPS files
 (where)        (what)             (how)         (output)

Step 1 — System: where the output goes

from AutoPoly import System

system = System(out="my_simulation")

System is a lightweight container for the output directory path. Everything AutoPoly writes lands under this folder. Create one per project.

Step 2 — Polymer / Molecule: what to build

Define each chemical species in the box. There are two classes, and you can mix them freely:

  • Polymer — polymer chains described by an explicit complement SMILES sequence (one entry per monomer). Controls chain count, topology (linear/ring), and tacticity.
  • Molecule — small molecules (solvents, additives) described by a regular SMILES string and a count.
from AutoPoly import Polymer, Molecule

polymer = Polymer(
    chain_num=10,
    sequence=["CC[*]"] + ["[*]CC[*]"] * 48 + ["[*]CC"],
    topology="linear",
    tacticity="atactic",
)

water = Molecule(Count=100, Smiles="O", Name="water")

The degree of polymerization is never specified directly — it is always len(sequence).

Step 3 — generate: how to build it

from AutoPoly import generate

generate(
    system,
    "polyethylene",
    [polymer, water],
    force_field="oplsaa",
)

generate takes the list of models and runs the full three-stage pipeline (Geometry → Typing → Packing):

  1. Monomer generation — each unique complement SMILES becomes a moltemplate .lt template (six variants per monomer: first/middle/last × two chiralities), with 3D geometry from RDKit.
  2. Atom typing & parameters — the force field manager assigns atom types from SMARTS patterns and collects bond/angle/dihedral/LJ parameters for the six supported force fields.
  3. Chain placement — chains are grown monomer-by-monomer with the Monte Carlo self-avoiding-walk algorithm (or placed on a deterministic grid) inside a sized simulation box.
  4. Moltemplate — the assembled system.lt is compiled into a LAMMPS data file.
  5. Output organization — system.data, system.in.init, system.in.settings, and system.in.charges are written to <System out>/<name>/.

Need more than one force field?

generate is the one-shot path. For stage-level control — e.g. building the geometry once and typing it under several force fields — use the GeometryBuilder / UnitTyper / BoxPacker classes from AutoPoly.pipeline directly.

See Output Files for what each file contains.

The coarse-grained exception

BeadSpringPolymer skips this pipeline entirely: it needs no SMILES, no atom typing, and no moltemplate. It writes a LAMMPS data file directly. See the Bead-Spring guide.

Where to go next