"""Defined interactions between two bonded partners."""
from typing import Optional, Tuple
import unyt as u
from gmso.core.parametric_potential import ParametricPotential
from gmso.utils.expression import PotentialExpression
try:
from pydantic.v1 import Field
except ImportError:
from pydantic import Field
[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 gmso.AtomType.name "
"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,
tags=None,
):
super(BondType, self).__init__(
name=name,
expression=expression,
parameters=parameters,
independent_variables=independent_variables,
potential_expression=potential_expression,
member_types=member_types,
member_classes=member_classes,
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_")
@staticmethod
def _default_potential_expr():
return PotentialExpression(
expression="0.5 * k * (r-r_eq)**2",
independent_variables={"r"},
parameters={
"k": 1000 * u.Unit("kJ / (nm**2)"),
"r_eq": 0.14 * u.nm,
},
)
[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_",
}