"""Defined interactions for improper-style connections."""
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 IMPROPER_TYPE_DICT
[docs]class ImproperType(ParametricPotential):
__base_doc__ = """A description of the interaction between 4 bonded partners.
This is a subclass of the gmso.core.Potential superclass.
ImproperType represents a improper 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 improper type are
stored as `member_types`.
The connectivity of an improper is:
m2
|
m1
/ \
m3 m4
where m1, m2, m3, and m4 are connection members 1-4, respectively.
Notes
----
Inherits many functions from gmso.ParametricPotential:
__eq__, _validate functions
"""
member_types_: Optional[Tuple[str, str, str, str]] = Field(
None,
description="List-like of gmso.AtomType.name "
"defining the members of this improper type",
)
member_classes_: Optional[Tuple[str, str, str, str]] = Field(
None,
description="List-like of gmso.AtomType.atomclass "
"defining the members of this improper type",
)
def __init__(
self,
name="ImproperType",
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 * ((phi - phi_eq))**2"
if parameters is None:
parameters = {
"k": 1000 * u.Unit("kJ / (deg**2)"),
"phi_eq": 0 * u.deg,
}
if independent_variables is None:
independent_variables = {"phi"}
super(ImproperType, 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=IMPROPER_TYPE_DICT,
tags=tags,
)
@property
def member_types(self):
"""Return member information for this ImproperType."""
return self.__dict__.get("member_types_")
@property
def member_classes(self):
return self.__dict__.get("member_classes_")
[docs] class Config:
"""Pydantic configuration for attributes."""
fields = {
"member_types_": "member_types",
"member_classes_": "member_classes",
}
alias_to_fields = {
"member_types": "member_types_",
"member_classes": "member_classes_",
}