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MC Placement & Chain Growth

AutoPoly builds the initial configuration of your simulation box with Monte Carlo (MC) methods: chains are grown monomer-by-monomer as self-avoiding walks (SAW), and whole molecules are placed with collision detection. The result is a coiled, overlap-free starting structure that equilibrates far faster than a grid or an extended chain.

Placement methods

Choose with the strategy parameter of generate:

Value Behavior
"mc_random" (default) Monte Carlo placement with SAW chain growth — realistic coiled conformations
"grid" Deterministic grid placement — extended chains on a lattice; simple, but far from equilibrium
"on_substrate" Film on a physical substrate slab — auto-selected when substrate= is passed; see Substrates & Films 
from AutoPoly import generate, GeometryConfig

generate(
    system,
    "polymer_mc",
    [polymer],
    force_field="oplsaa",
    strategy="mc_random",                 # Monte Carlo placement (default)
    mc_max_attempts=10000,                # max placement attempts
    monomer_density=0.085,                # target density (monomers / ų)
    geometry_config=GeometryConfig(
        use_mc_chain_growth=True,         # SAW chain growth (default)
        mc_bond_angle_min=50.0,           # min deflection angle (degrees)
        mc_bond_angle_max=90.0,           # max deflection angle (degrees)
    ),
)

How SAW chain growth works

  1. Each chain starts from a random seed monomer.
  2. Every next monomer is attached at a random orientation within the allowed deflection angle window (mc_bond_angle_min … mc_bond_angle_max). Deflection = 180° − bond angle, so a tetrahedral carbon corresponds to ≈ 70.5°.
  3. A cell-linked-list collision detector rejects placements that overlap existing atoms — both other chains and, with mc_intrachain_exclude_neighbors (default 2), the growing chain itself beyond its bonded neighbors.
  4. If no valid position is found within mc_max_attempts, growth backtracks and retries.

Set use_mc_chain_growth=False in the GeometryConfig to place whole chains rigidly instead of growing them.

Box sizing

Boxes are sized from SAW scaling — N^0.6 × bond_length for a chain of N monomers — combined with the target monomer_density, rather than the fully extended chain length. This produces compact, realistic boxes at low initial density, leaving room for overlap-free placement before NPT compression.

Tuning guide

Symptom Knob
Placement fails / "max attempts exceeded" Lower monomer_density (looser box), raise mc_max_attempts
Chains too extended or too knotted Adjust mc_bond_angle_min/max in GeometryConfig toward your chemistry's real bond angles
False-positive collisions along a chain Raise mc_intrachain_exclude_neighbors in GeometryConfig (2 is recommended)
Want reproducible grid layout strategy="grid"

The mc module

The placement engine is a standalone subpackage — see the mc API reference for CollisionDetector, ChainGrowthMC, and MolecularPlacementMC. The same collision machinery drives bead-spring generation.

See also