Biochar Simulator

Getting Started

  • Installation
    • Requirements
    • conda (recommended)
    • From PyPI
    • Development install
  • Quick Start
    • From pyrolysis temperature and feedstock
    • Single molecule
    • With functional groups
    • With pentagon defects
    • Slit-pore surface
    • Run in GROMACS

User Guide

  • Single Molecule Generation
    • Generation pipeline
    • Controlling size
      • PAH library (seed molecules)
    • Controlling composition
    • Pentagon ring defects
    • Reproducibility
    • Using the class API
  • Functional Groups
    • Two modes
    • Available groups
    • Ether bridge geometry
    • Mixing group types
  • Porous Surface Generation
    • Symmetric slit pore
    • Asymmetric pore
    • Multi-sheet stacking
    • Using the class API
    • Output files
  • Batch Generation
    • Temperature series
    • Configuration dict keys
    • Running a mixed GROMACS simulation
  • GROMACS Workflow
    • 1. Generate the structure
    • 2. Energy minimisation
    • 3. Visualise
    • 4. Solvation (optional)
    • 5. Production MD
    • Force field notes

Examples

  • Biochar Structure Visualization Demo
    • Helper: 3D viewer
    • 1 Single molecule — 2D structure
    • 2 Single molecule — interactive 3D
    • 3 Functional group comparison
    • 4 Pentagon ring defects
    • 5 Slit-pore surface
    • 6 Temperature series — van Krevelen diagram
    • 7 Asymmetric slit-pore surface

API Reference

  • biochar_generator
    • Convenience functions
      • generate_biochar()
      • generate_surface()
      • generate_biochar_series()
    • Configuration
      • GeneratorConfig
        • GeneratorConfig.target_num_carbons
        • GeneratorConfig.size_tolerance
        • GeneratorConfig.H_C_ratio
        • GeneratorConfig.H_C_tolerance
        • GeneratorConfig.O_C_ratio
        • GeneratorConfig.O_C_tolerance
        • GeneratorConfig.aromaticity_percent
        • GeneratorConfig.aromaticity_tolerance
        • GeneratorConfig.functional_groups
        • GeneratorConfig.periodic_box
        • GeneratorConfig.box_size
        • GeneratorConfig.molecule_name
        • GeneratorConfig.seed
        • GeneratorConfig.defect_fraction
        • GeneratorConfig.max_ether_span
    • Class API
      • BiocharGenerator
        • BiocharGenerator.generate()
        • BiocharGenerator.export_gromacs()
        • BiocharGenerator.print_summary()
  • temperature_model
    • Module-level helpers
      • properties()
      • VALID_FEEDSTOCKS
    • TemperatureModel
      • TemperatureModel
        • TemperatureModel.predict()
        • TemperatureModel.aromaticity_from_hc()
        • TemperatureModel.composition()
        • TemperatureModel.predict_all()
        • TemperatureModel.feedstocks
        • TemperatureModel.provenance
    • Build helper
      • build_model()
      • compare_models()
  • surface_builder
    • Configuration & data classes
      • SurfaceConfig
        • SurfaceConfig.target_num_carbons
        • SurfaceConfig.H_C_ratio
        • SurfaceConfig.O_C_ratio
        • SurfaceConfig.functional_groups
        • SurfaceConfig.aromaticity_percent
        • SurfaceConfig.pore_type
        • SurfaceConfig.num_sheets
        • SurfaceConfig.pore_diameter
        • SurfaceConfig.max_attempts
        • SurfaceConfig.min_separation
        • SurfaceConfig.sheet_overrides
        • SurfaceConfig.box_padding_xy
        • SurfaceConfig.box_padding_z
        • SurfaceConfig.system_name
        • SurfaceConfig.sheet_base_name
        • SurfaceConfig.seed
        • SurfaceConfig.defect_fraction
      • SheetResult
        • SheetResult.mol
        • SheetResult.coords
        • SheetResult.composition
        • SheetResult.atom_types
        • SheetResult.charges
        • SheetResult.molecule_name
    • Builder
      • SurfaceBuilder
        • SurfaceBuilder.build()
        • SurfaceBuilder.export_gromacs()
  • gromacs_export
    • GromacsExporter
      • GromacsExporter.export()
    • GROFileWriter
      • GROFileWriter.write()
    • TOPFileWriter
      • TOPFileWriter.write()
    • ITPFileWriter
      • ITPFileWriter.write()
    • MultiSheetGROWriter
      • MultiSheetGROWriter.write()
    • SurfaceTopologyWriter
      • SurfaceTopologyWriter.write()
  • opls_typing
    • AtomTyper
      • AtomTyper.assign_atom_types()
      • AtomTyper.get_bond_parameters()
      • AtomTyper.get_angle_parameters()
    • ChargeAssigner
      • ChargeAssigner.assign_charges()
  • constants
    • get_atom_mass()
    • get_vdw_radius()
    • get_covalent_radius()

Development

  • Changelog
    • 0.2.0 (2026-06-01)
    • 0.1.4 (2026-05-31)
    • 0.1.3 (2026-05-29)
    • 0.1.1 (2026-04-18)
    • 0.1.0 (2026-04-17)
Biochar Simulator
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