constants

OPLS-AA force field parameters, PAH library entries, and physical constants used throughout the package.

OPLS-AA parameters

OPLS_ATOM_TYPES

dict[str, tuple] — atom type → (description, mass_amu, default_charge)

GROMACS_OPLS_TYPE_MAP

dict[str, str] — internal atom type → GROMACS opls_XXX name.

Note

Lennard-Jones, bond, and angle parameters are not stored in this module. An exported topology #includes a real oplsaa.ff, and GROMACS resolves every one of those parameters from it by the opls_XXX name above. Earlier releases carried hand-copied OPLS_LJ_PARAMS, OPLS_BOND_PARAMS and OPLS_ANGLE_PARAMS tables; they were unused by the exporter and had drifted from the force field, so they were removed. Supply any parameter the force field lacks via a local .itp rather than reinstating a table here.

Functional groups

FUNCTIONAL_GROUPS

dict[str, dict] — group name → definition dict with keys atoms, connectivity, composition, O_per_group, H_per_group.

PAH library

PAH_LIBRARY

dict[str, dict] — molecule name → {smiles, num_atoms, num_aromatic, molecular_formula, references}. Contains 18 validated entries from benzene (6 C) to hex_lattice_40 (40 C).

Physical constants

CARBON_VDW_DIAMETER

float — 3.4 Å — graphite interlayer spacing, used as effective sheet thickness when computing slit-pore geometry.

Helper functions

biochar.constants.get_atom_mass(atom_type)

Get atomic mass from OPLS atom type.

Return type:

float

Parameters:

atom_type (str)

biochar.constants.get_vdw_radius(element)

Get Van der Waals radius for element.

Return type:

float

Parameters:

element (str)

biochar.constants.get_covalent_radius(element)

Get covalent radius for element.

Return type:

float

Parameters:

element (str)