Block Copolymer (PE-PS-PE)

Block copolymers are where complement SMILES shines: the sequence list gives you explicit control over the monomer at every position, so any block arrangement is just a matter of listing monomers in order.

This example builds a PE-PS-PE ABA triblock: polyethylene end blocks flanking a polystyrene mid-block.

You will learn:

• How to write a mixed-monomer sequence with clean block boundaries
• Why internal positions always need two wildcards, even across a block boundary
• How block lengths follow directly from list repetition counts

The script

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Example: Creating an ABA triblock copolymer with explicit monomer sequences.

This example demonstrates how to create block copolymers with precise
monomer placement at each position in the polymer chain.

The new explicit sequence API allows you to:
- Create block copolymers (e.g., ABA triblock)
- Specify exact monomer at each position
- Create arbitrary sequences

Created on 2026-01-13
@author: zwu
"""

from AutoPoly import System, Polymer, generate

# Create system
system = System(out="aba_triblock")

# Define explicit monomer sequence with complement SMILES format
# ABA triblock: 2 PE-like, 3 PS-like, 2 PE-like
# This creates a block copolymer structure
# Complement SMILES: first position has 1 wildcard (right), middle have 2, last has 1 (left)
sequence = [
    "CC[*]",                # Position 0: Ethylene - First (1 wildcard right)
    "[*]CC[*]",             # Position 1: Ethylene - Middle (2 wildcards)
    "[*]CC(c1ccccc1)[*]",   # Position 2: Styrene - Middle (2 wildcards)
    "[*]CC(c1ccccc1)[*]",   # Position 3: Styrene - Middle (2 wildcards)
    "[*]CC(c1ccccc1)[*]",   # Position 4: Styrene - Middle (2 wildcards)
    "[*]CC[*]",             # Position 5: Ethylene - Middle (2 wildcards)
    "[*]CC"                 # Position 6: Ethylene - Last (1 wildcard left)
]

# Create polymer with explicit sequence
poly = Polymer(
    chain_num=5,
    sequence=sequence,  # DOP is automatically 7
    topology="linear",
    tacticity="atactic"
)

# Print polymer information
print(f"Created ABA triblock copolymer:")
print(f"  Number of chains: {poly.chain_num}")
print(f"  DOP (degree of polymerization): {poly.dop}")
print(f"  Unique monomer types: {poly.mer_set}")
print(f"  Topology: {poly.topology}")
print(f"  Tacticity: {poly.tacticity}")

# You can also use get_chain_info() for complete information
info = poly.get_chain_info()
print(f"\nComplete chain info:")
for key, value in info.items():
    print(f"  {key}: {value}")

# Run the generation — this creates the LAMMPS input files
# (monomer templates -> chain growth -> moltemplate -> system.data)
generate(system, "aba_triblock", [poly], force_field="oplsaa")

print(f"\nLAMMPS input files written to: aba_triblock/aba_triblock/")
print(f"  system.data          topology + coordinates (read_data)")
print(f"  system.in.init       units / atom / bond styles")
print(f"  system.in.settings   force-field parameters")
print(f"\nQuick check: each chain should have 74 atoms (C32H42) with")
print(f"3 phenyl rings from the styrene middle units.")

Run it

cd examples
python example_block_copolymer.py

Variations to try

• Change the block length ratio (e.g. symmetric 10-20-10 vs asymmetric 5-30-5)
• Make a diblock (PE-PS) by ending the sequence with a PS last variant
• Make an alternating copolymer by interleaving single monomers — see Common Patterns