biochar 0.1.3

Generate biochar molecular structures for GROMACS MD simulations

Biochar Simulator — Structure Generator

A Python package for generating realistic biochar molecular structures for GROMACS molecular dynamics simulations. Supports single molecules, temperature/composition series, and porous slit-pore surfaces.

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Overview

The Biochar Simulator builds polycyclic aromatic hydrocarbon (PAH) structures with user-specified compositional parameters and exports GROMACS-ready force field files. Supports both pure hexagonal aromatic skeletons and topologically disordered structures with pentagon ring defects.

Key capabilities:

• Size: 6 to 200+ carbons (exact count for most targets)
• Composition: H/C and O/C ratios with configurable tolerances
• Aromaticity: 100% aromatic skeleton (graphene-nanoflake topology, or defective with pentagons)
• Ring Defects: Optional pentagon insertion during graph growth (defect_fraction parameter)
• Functional Groups: Exact counts via dict API — phenolic, carboxyl, ether, carbonyl, quinone, lactone, hydroxyl
• Porous Surfaces: Slit-pore systems of stacked PAH sheets with user-controlled pore diameter
• Output: GROMACS .gro, .top, .itp files with OPLS-AA force field

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Installation

conda (recommended)

conda install -c conda-forge biochar

PyPI

pip install biochar

Requirements

• Python 3.9+
• RDKit ≥ 2023.9
• NumPy ≥ 1.24, SciPy ≥ 1.10, NetworkX ≥ 3.1

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Quick Start

Single molecule

from biochar.biochar_generator import generate_biochar

mol, coords, gro_path, top_path, itp_path = generate_biochar(
    target_num_carbons=100,
    H_C_ratio=0.5,
    O_C_ratio=0.1,
    output_directory="output",
    basename="biochar_100C",
    seed=42,
)

With specific functional groups

Use a dict to place exact counts of each group type:

mol, coords, gro, top, itp = generate_biochar(
    target_num_carbons=50,
    functional_groups={"phenolic": 3, "carboxyl": 1, "ether": 2},
    output_directory="output",
    basename="biochar_fg",
    seed=42,
)

When functional_groups is None (default), total oxygen is controlled by O_C_ratio and placed as phenolic groups.

With pentagon ring defects

Add topological disorder by inserting 5-membered rings during growth:

# ~15% of rings will be pentagons instead of hexagons
mol, coords, gro, top, itp = generate_biochar(
    target_num_carbons=60,
    defect_fraction=0.15,  # probability per ring addition
    output_directory="output",
    basename="biochar_defects",
    seed=42,
)

defect_fraction ranges from 0.0 (pure hexagonal PAH) to 1.0 (all pentagons). Typical values: 0.1–0.2.

Slit-pore surface

from biochar.biochar_generator import generate_surface

# Two identical sheets, 10 Å pore
sheets, gro, top, itps = generate_surface(
    target_num_carbons=50,
    functional_groups={"phenolic": 2, "ether": 1},
    pore_diameter=10.0,
    output_directory="output",
    basename="slit_pore",
    seed=42,
)

# Asymmetric pore — different chemistry on each wall
sheets, gro, top, itps = generate_surface(
    pore_diameter=8.0,
    sheet_overrides=[
        {"functional_groups": {"phenolic": 3}, "target_num_carbons": 40},
        {"functional_groups": {"carboxyl": 2}, "target_num_carbons": 50},
    ],
    output_directory="output",
    basename="asymmetric_pore",
)

Batch generation (temperature/composition series)

from biochar.biochar_generator import generate_biochar_series

configs = [
    {"molecule_name": "BC400", "target_num_carbons": 80,  "H_C_ratio": 0.65, "O_C_ratio": 0.20, "seed": 1},
    {"molecule_name": "BC600", "target_num_carbons": 100, "H_C_ratio": 0.55, "O_C_ratio": 0.12, "seed": 2},
    {"molecule_name": "BC800", "target_num_carbons": 120, "H_C_ratio": 0.40, "O_C_ratio": 0.05, "seed": 3},
]

results = generate_biochar_series(
    configurations=configs,
    output_directory="output/temperature_series",
    create_combined_top=True,   # writes combined.top
)

Then run in GROMACS:

cd output/temperature_series
gmx grompp -f md.mdp -p combined.top -o topol.tpr
gmx mdrun -deffnm topol

---

Configuration Parameters

Single molecule (GeneratorConfig / generate_biochar)

Parameter	Type	Default	Description
target_num_carbons	int	50	Target carbon count
H_C_ratio	float	0.5	Target H/C molar ratio
H_C_tolerance	float	0.10	Allowed H/C error (fraction)
O_C_ratio	float	0.1	Target O/C molar ratio
O_C_tolerance	float	0.10	Allowed O/C error (fraction)
aromaticity_percent	float	90.0	Target % aromatic carbons
functional_groups	dict|None	None	Exact group counts, e.g. {"phenolic": 2}
defect_fraction	float	0.0	Probability [0, 1) each ring is a pentagon
molecule_name	str	"BC"	Residue name (≤5 chars for GROMACS)
periodic_box	bool	False	Add periodic box vectors to .gro
seed	int|None	None	RNG seed for reproducibility

Slit-pore surface (SurfaceConfig / generate_surface)

Parameter	Type	Default	Description
target_num_carbons	int	50	Carbons per sheet
H_C_ratio	float	0.3	Target H/C per sheet
O_C_ratio	float	0.05	Target O/C per sheet
functional_groups	dict|None	None	Groups applied to all sheets
defect_fraction	float	0.0	Pentagon probability per ring per sheet
pore_diameter	float	10.0	Gap between sheet surfaces (Å)
num_sheets	int	2	Number of parallel sheets
sheet_overrides	list|None	None	Per-sheet config dicts (length = num_sheets)
box_padding_xy	float	1.0	Box padding in x/y (nm)
box_padding_z	float	1.0	Box padding in z (nm)
system_name	str	"SLIT"	Name in .top [ system ] section
sheet_base_name	str	"SHT"	Residue name base (≤3 chars)
seed	int|None	None	RNG seed

Available functional groups

Group	O added	Notes
"phenolic"	1	Ar–OH; always works
"hydroxyl"	1	Same as phenolic for pure PAH
"carboxyl"	2	Ar–C(=O)(OH); adds extra C
"ether"	1	Ar–O–Ar bridge across two edge sites
"carbonyl"	1	Falls back to phenolic with warning
"quinone"	2	Falls back to phenolic with warning
"lactone"	2	Falls back to phenolic with warning

Carbonyl, quinone, and lactone require ≥2 free valence on one carbon, which is unavailable on pure aromatic PAH edge sites — they warn and substitute phenolic automatically.

---

Generation Pipeline

Single molecule

target_num_carbons
      │
      ▼
Carbon skeleton (PAH seed + ring-growth)
      │  Parity-aware hex-lattice builder; 100% aromatic for any size
      ▼
Oxygen assignment (functional groups dict or O/C-ratio-driven)
      │
      ▼
Hydrogen assignment (fill valences → target H/C ratio)
      │
      ▼
3D geometry
      │  ≤80 heavy atoms: ETKDGv3 / ETKDGv2 embedding + MMFF94
      │  >80 heavy atoms: 2D-first embedding (flat graphene sheet) + FF minimisation
      ▼
OPLS-AA atom typing & partial charges
      │
      ▼
Validation (composition, geometry, steric clashes)
      │
      ▼
GROMACS export (.gro / .top / .itp)

Slit-pore surface

SurfaceConfig
      │
      ▼
Generate N sheets (each via single-molecule pipeline above)
      │  Identical sheets: generate once, deep-copy remainder
      │  Distinct sheets:  generate each independently
      ▼
Flatten each sheet to xy plane (SVD best-fit plane rotation)
      │
      ▼
Stack along z: sheet_i centroid at z = i × (pore_diameter + 3.4 Å)
      │
      ▼
Compute periodic box (bounding box + padding)
      │
      ▼
Centre system in box
      │
      ▼
GROMACS export
      │  .gro  — all N sheets as separate residues, single file
      │  .itp  — one file (identical sheets) or one per sheet (distinct)
      └─ .top  — includes forcefield + itp(s); [ molecules ] count = N

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Supported Sizes

Range	Strategy	Aromaticity	Count accuracy
6–40 C	Exact PAH library match	100%	Exact
41–200+ C	Library seed + 4-node ring growth	100%	≤5% error

PAH library (18 validated entries)

Molecule	Carbons	Type
benzene	6	Classic
naphthalene	10	Classic
anthracene / phenanthrene	14	Linear / angular
pyrene	16	Pericondensed
chrysene / tetracene / triphenylene	18	Various
pentacene / picene / hex_lattice_22	22	Various
coronene	24	7-ring pericondensed
hexacene / dibenzo_bc_ef_coronene	26	Various
hex_lattice_28	28	Compact nanoflake
hex_lattice_30	30	Compact nanoflake
hex_lattice_38	38	Compact nanoflake
hex_lattice_40	40	Compact nanoflake

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Typical H/C ratios by pyrolysis temperature

Temperature	H/C	O/C	Notes
300–400 °C	0.6–0.8	0.15–0.25	Partially carbonised, high O
500–600 °C	0.4–0.6	0.08–0.15	Moderately graphitic
700–800 °C	0.2–0.4	0.02–0.08	Highly graphitic, low O

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Output Files

File	Format	Contents
.gro	GROMACS structure	Atom positions in nm, box vectors
.top	GROMACS topology	Force field include, molecule definitions
.itp	Include topology	Atoms, bonds, angles, dihedrals for one molecule type

Coordinates are in nanometers (GROMACS convention; RDKit Å × 0.1).

For surfaces, a single .gro contains all sheets as separate residues, and the .top references one .itp with a molecule count (identical sheets) or one .itp per unique sheet type.

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Source Modules

Module	Responsibility
carbon_skeleton.py	PAH library lookup and ring-growth engine
heteroatom_assignment.py	Oxygen (functional groups) and hydrogen placement
geometry_3d.py	3D coordinate generation and clash resolution
opls_typing.py	OPLS-AA atom types and partial charges
gromacs_export.py	.gro / .top / .itp writers (single and multi-sheet)
surface_builder.py	Slit-pore surface assembly (SurfaceBuilder, SurfaceConfig)
validation.py	Composition, chemistry, and geometry checks
constants.py	OPLS-AA parameters, PAH library, VdW radii
biochar_generator.py	Public API: generate_biochar, generate_surface, generate_biochar_series

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Testing

# Unit tests (constants, skeleton, heteroatoms, geometry, OPLS, validation, generator)
python3 -m pytest tests/test_generator.py -v

# Surface builder tests (config, geometry, GROMACS export, convenience function)
python3 -m pytest tests/test_surface_builder.py -v

# PAH quality suite (sizes 6–200C, compositions, seeds)
python3 tests/test_pah_quality.py

The PAH quality suite reports:

• PAH library SMILES validity and kekulizability
• Atom count accuracy (target vs actual)
• Bond errors and steric clashes per size
• Ring planarity (Å deviation from best-fit plane)
• H/C and O/C ratio accuracy across compositions

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Known Limitations

Issue	Notes
H/C ratio loose for very small structures (6–14 C)	Edge-to-interior carbon ratio limits control; use ≥30 C for tight H/C
Steric clash count increases with size	Large flat aromatics have H···H near-contacts; use GROMACS energy minimisation after generation for production runs
Geometry validation thresholds	The built-in validator uses strict VdW radii; some reported "clashes" are artefacts of the flat starting structure and resolve under MD
Amorphous porous surfaces not yet implemented	Only slit pores (parallel sheets) are supported; pore_type="amorphous" is reserved for a future release

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References

• Jorgensen, W. L. et al. "Development and Testing of the OPLS All-Atom Force Field." J. Am. Chem. Soc. 118.45 (1996): 11225–11236.
• RDKit: Open-source cheminformatics. https://www.rdkit.org