Source code for gmso.core.bond_type

"""Defined interactions between two bonded partners."""
from typing import Optional, Tuple

import unyt as u
from pydantic import Field

from gmso.core.parametric_potential import ParametricPotential
from gmso.utils._constants import BOND_TYPE_DICT

[docs]class BondType(ParametricPotential): __base_doc__ = """A descripton of the interaction between 2 bonded partners. This is a subclass of the gmso.core.Potential superclass. BondType represents a bond type and includes the functional form describing its interactions. The functional form of the potential is stored as a `sympy` expression and the parameters, with units, are stored explicitly. The AtomTypes that are used to define the bond type are stored as `member_types`. Notes ---- Inherits many functions from gmso.ParametricPotential: __eq__, _validate functions """ member_types_: Optional[Tuple[str, str]] = Field( None, description="List-like of of " "defining the members of this bond type", ) member_classes_: Optional[Tuple[str, str]] = Field( None, description="List-like of of gmso.AtomType.atomclass " "defining the members of this bond type", ) def __init__( self, name="BondType", expression=None, parameters=None, independent_variables=None, potential_expression=None, member_types=None, member_classes=None, topology=None, tags=None, ): if potential_expression is None: if expression is None: expression = "0.5 * k * (r-r_eq)**2" if parameters is None: parameters = { "k": 1000 * u.Unit("kJ / (nm**2)"), "r_eq": 0.14 * u.nm, } if independent_variables is None: independent_variables = {"r"} super(BondType, self).__init__( name=name, expression=expression, parameters=parameters, independent_variables=independent_variables, potential_expression=potential_expression, topology=topology, member_types=member_types, member_classes=member_classes, set_ref=BOND_TYPE_DICT, tags=tags, ) @property def member_types(self): """Return the members involved in this bondtype.""" return self.__dict__.get("member_types_") @property def member_classes(self): return self.__dict__.get("member_classes_")
[docs] class Config: """Pydantic configuration for class attributes.""" fields = { "member_types_": "member_types", "member_classes_": "member_classes", } alias_to_fields = { "member_types": "member_types_", "member_classes": "member_classes_", }