Biochar Simulator

A Python package for generating realistic biochar molecular structures for GROMACS molecular dynamics simulations.

from biochar import generate_biochar

mol, coords, gro, top, itp = generate_biochar(
    target_num_carbons=80,
    H_C_ratio=0.5,
    O_C_ratio=0.10,
    functional_groups={"phenolic": 3, "carboxyl": 1},
    output_directory="output",
    seed=42,
)

Key features

  • PAH skeletons from 6 to 200+ carbons with exact carbon counts

  • H/C and O/C ratio control with configurable tolerances

  • Data-driven composition from pyrolysis temperature and feedstock (UC Davis Biochar Database)

  • Functional groups: phenolic, carboxyl, ether, thiol, thioether, amino, and ring-N doping

  • Pentagon ring defects for realistic topological disorder

  • Slit-pore and amorphous surface systems

  • GROMACS-ready .gro / .top / .itp with OPLS-AA force field

Getting Started

User Guide

Examples

API Reference

Development

Indices and tables