PolyMCsim

A high-performance Python library for computational chemists to generate polymer graph structures through Monte Carlo simulations. The library models polymerization reactions using monomers as nodes and chemical bonds as edges, enabling emergent generation of diverse polymer architectures.

Features

• Monte Carlo simulation of polymer growth
• Numba-optimized performance
• JSON/Pydantic configuration
• Batch simulation capabilities
• Support for complex monomer structures
• Parallel processing for large-scale simulations

Installation

PolyMCsim requires Python 3.8 or later. To install, run:

# Using Poetry (recommended)
poetry install

# Using pip
pip install .

Development Setup

1. Install Poetry (if not already installed):

   curl -sSL https://install.python-poetry.org | python3 -
   

2. Clone the repository:

   git clone <repository-url>
   cd polymcsim
   

3. Install dependencies:

   poetry install
   

4. Install pre-commit hooks:

   poetry run pre-commit install
   

Usage

Basic example of polymer generation:

from polymcsim import PolymerSimulation

# Configure simulation
sim = PolymerSimulation(
    monomers_config="path/to/monomers.json",
    n_steps=1000
)

# Run simulation
result = sim.run()

# Export results
result.export_graph("polymer.graphml")

Testing

Run the test suite:

poetry run pytest

License

[License Type] - See LICENSE file for details

Contributing

Contributions are welcome! Please read our Contributing Guidelines for details on how to submit pull requests, report issues, and contribute to the project.

• High Performance: Built with Numba for C-like speed in computationally intensive parts.
• Extensible: Easily define new monomer types, reactions, and simulation parameters.
• Rich Visualization: Generate insightful plots and analyses right out of the box.

For detailed information, visit the full documentation at juliankimmig.github.io/polymcsim/.

Installation

You can install polymcsim via pip:

pip install polymcsim

Alternatively, you can use uv:

uv pip install polymcsim

Quick Start

Here's a minimal example of how to simulate the formation of a branched polymer and visualize its structure:

from polymcsim import PolymerSimulation

# 1. Define monomers and reactions
monomers = [
    # ... existing code ...
    # 4. Run the simulation
    sim = PolymerSimulation(simulation_input)
    polymer_graph = sim.run()

    # 5. Visualize the largest polymer structure
    sim.visualize_polymer(polymer_graph)

This will produce an image of the largest polymer's network structure. polymcsim also offers more advanced visualizations, such as molecular weight distribution plots and comprehensive analysis dashboards.