AutoPoly: Automated Polymer Generation and Simulation Package

AutoPoly is a comprehensive Python package for generating polymer structures and preparing them for molecular dynamics simulations using LAMMPS and Moltemplate.

Overview

AutoPoly provides tools for:

• Polymer Structure Generation: Create atomistic polymer models with various topologies and tacticity
• Force Field Integration: Seamless integration with OPLS-AA and LOPLS force fields
• LAMMPS Preparation: Generate complete LAMMPS input files and data structures
• Bead-Spring Models: Simplified coarse-grained polymer models for quick simulations
• File Management: Automated organization of simulation files and outputs

Key Features

🧬 Polymer Topologies

• Linear Polymers: Standard linear chain structures
• Ring Polymers: Circular polymer topologies
• Custom Sequences: User-defined monomer sequences

🎯 Tacticity Control

• Atactic: Random stereochemistry
• Isotactic: All monomers with same stereochemistry
• Syndiotactic: Alternating stereochemistry

🔬 Force Fields

• OPLS-AA: All-atom force field for accurate simulations
• LOPLS: Lipid-optimized force field variant
• Custom Parameters: Support for modified force field parameters

📁 File Management

• Monomer Bank: Centralized monomer template library
• Output Organization: Structured file organization
• Error Handling: Comprehensive validation and error reporting

Installation

Prerequisites

• Python 3.7+
• LAMMPS (for simulations)
• Moltemplate (for structure generation)

Install AutoPoly

# Clone the repository
git clone <repository-url>
cd AutoPoly

# Install the package
pip install -e .

Quick Start

1. Basic Polymer Generation

from AutoPoly import System, Polymer, Polymerization

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

# Define polymer
polymer = Polymer(
    ChainNum=10,
    Sequence=["ethylene"],
    DOP=100,
    topology="linear",
    tacticity="atactic"
)

# Generate structure
polymerization = Polymerization(
    name="ethylene_polymer",
    system=system,
    model=[polymer]
)

2. Bead-Spring Model

from AutoPoly import BeadSpringPolymer, System

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

# Generate bead-spring polymer
bead_polymer = BeadSpringPolymer(
    name="test_polymer",
    system=system,
    n_chains=5,
    n_beads=20,
    topology="linear"
)

# Generate LAMMPS files
bead_polymer.generate_data_file()

3. Ring Polymer

# Create ring polymer
ring_polymer = Polymer(
    ChainNum=5,
    Sequence=["styrene"],
    topology="ring",
    tacticity="atactic"
)

# Generate with polymerization
polymerization = Polymerization(
    name="ring_styrene",
    system=system,
    model=[ring_polymer]
)

Package Structure

AutoPoly/
├── AutoPoly/
│   ├── __init__.py          # Package initialization
│   ├── system.py            # System management
│   ├── polymer.py           # Polymer definition
│   ├── polymerization.py    # Core polymerization logic
│   ├── bead_spring.py       # Bead-spring models
│   ├── conf.py              # Configuration settings
│   ├── logger.py            # Logging utilities
│   └── extern/              # External dependencies
│       ├── Monomer_bank/    # Monomer templates
│       ├── moltemplate/     # Moltemplate files
│       └── rdlt.py          # LAMMPS data utilities
├── examples/                # Usage examples
├── tests/                   # Test suite
└── docs/                    # Documentation

Core Classes

System

Manages file paths and directory operations for polymer simulations.

system = System(out="output_directory")

Polymer

Defines polymer properties including topology, tacticity, and monomer sequences.

polymer = Polymer(
    ChainNum=10,           # Number of chains
    Sequence=["monomer"],  # Monomer sequence
    DOP=100,              # Degree of polymerization
    topology="linear",     # "linear" or "ring"
    tacticity="atactic"    # "atactic", "isotactic", "syndiotactic"
)

Polymerization

Core class for generating polymer structures using Moltemplate.

polymerization = Polymerization(
    name="project_name",
    system=system,
    model=[polymer],
    is_lopls=False  # Use LOPLS force field
)

BeadSpringPolymer

Simplified bead-spring model generator for coarse-grained simulations.

bead_polymer = BeadSpringPolymer(
    name="model_name",
    system=system,
    n_chains=5,
    n_beads=20,
    topology="linear"
)

Configuration

Logging

Configure logging levels in conf.py:

LOG = {
    'ROOT_LEVEL': logging.INFO,
    'CONSOLE_LEVEL': logging.INFO,
    'FILE_LEVEL': logging.INFO,
    'TO_FILE': False
}

Output Paths

Set output directory in conf.py:

OUT_PATH = os.path.join(os.path.expanduser("~"))

Examples

Linear Polyethylene

from AutoPoly import System, Polymer, Polymerization

system = System(out="polyethylene")
polymer = Polymer(ChainNum=10, Sequence=["ethylene"], DOP=50)
polymerization = Polymerization(name="PE", system=system, model=[polymer])

Ring Polystyrene

polymer = Polymer(
    ChainNum=5,
    Sequence=["styrene"],
    topology="ring",
    tacticity="atactic"
)
polymerization = Polymerization(name="ring_PS", system=system, model=[polymer])

Copolymer

polymer = Polymer(
    ChainNum=10,
    Sequence=["ethylene", "propylene"],
    DOP=100,
    tacticity="syndiotactic"
)

Output Files

AutoPoly generates the following files:

LAMMPS Files

• system.data: Atom coordinates and connectivity
• system.in.settings: Force field parameters
• system.in.charges: Atomic charges
• system.in: LAMMPS input script
• system.in.init: Initialization script

Organization

project_name/
├── moltemplate/     # Intermediate files
├── input/          # Input templates
├── output/         # LAMMPS files
└── logs/           # Log files

Troubleshooting

Common Issues

1. Monomer Not Found

   • Check monomer bank path in extern/Monomer_bank/
   • Verify monomer file names match sequence

2. Moltemplate Errors

   • Ensure Moltemplate is properly installed
   • Check monomer .lt file syntax
   • Verify force field parameter files

3. File Permission Errors

   • Check write permissions for output directory
   • Ensure sufficient disk space

Debug Mode

Enable detailed logging:

from AutoPoly.conf import LOG
LOG['ROOT_LEVEL'] = logging.DEBUG
LOG['TO_FILE'] = True

Contributing

1. Fork the repository
2. Create a feature branch
3. Make your changes
4. Add tests
5. Submit a pull request

License

This project is licensed under the BSD License - see the license.md file for details.

Citation

If you use AutoPoly in your research, please cite:

@software{autopoly2024,
  title={AutoPoly: Automated Polymer Generation and Simulation Package},
  author={Wu, Zhenghao},
  year={2024},
  url={https://github.com/your-repo/autopoly}
}

Support

For questions and support:

• Check the documentation
• Review example files
• Open an issue on GitHub
• Contact the maintainers

Acknowledgments

• Moltemplate developers for the structure generation framework
• LAMMPS developers for the molecular dynamics engine
• OPLS-AA force field developers