Source code for gmso.core.dihedral_type

import warnings
import unyt as u

from gmso.core.potential import Potential
from gmso.exceptions import GMSOError
from gmso.utils._constants import DIHEDRAL_TYPE_DICT

[docs]class DihedralType(Potential): """A descripton of the interaction between 4 bonded partners. This is a subclass of the gmso.core.Potential superclass. DihedralType represents a dihedral 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 dihedral type are stored as `member_types`. The connectivity of a dihedral is: m1–m2–m3–m4 where m1, m2, m3, and m4 are connection members 1-4, respectively. Parameters ---------- name : str expression : str or sympy.Expression See `Potential` documentation for more information parameters : dict {str, unyt.unyt_quantity} See `Potential` documentation for more information independent vars : set of str See `Potential` documentation for more information member_types : list-like of str List-like of of defining the members of this dihedral type topology: gmso.core.Topology, default=None The topology of which this dihedral type is a part of set_ref: str The string name of the bookkeeping set in topology class. Notes ---- Inherits many functions from gmso.Potential: __eq__, _validate functions """ def __init__(self, name='DihedralType', expression='k * (1 + cos(n * phi - phi_eq))**2', parameters=None, independent_variables=None, member_types=None, topology=None, set_ref='dihedral_type_set'): if parameters is None: parameters = { 'k': 1000 * u.Unit('kJ / (deg**2)'), 'phi_eq': 180 * u.deg, 'n': 1 * u.dimensionless } if independent_variables is None: independent_variables = {'phi'} if member_types is None: member_types = list() super(DihedralType, self).__init__(name=name, expression=expression, parameters=parameters, independent_variables=independent_variables, topology=topology) self._set_ref = DIHEDRAL_TYPE_DICT self._member_types = _validate_four_member_type_names(member_types) @property def set_ref(self): return self._set_ref @property def member_types(self): return self._member_types @member_types.setter def member_types(self, val): if self.member_types != val: warnings.warn("Changing an DihedralType's constituent " "member types: {} to {}".format(self.member_types, val)) self._member_types = _validate_four_member_type_names(val) def __repr__(self): return "<DihedralType {}, id {}>".format(, id(self))
def _validate_four_member_type_names(types): """Ensure exactly 4 partners are involved in DihedralType""" if len(types) != 4 and len(types) != 0: raise GMSOError("Trying to create an DihedralType " "with {} constituent types".format(len(types))) if not all([isinstance(t, str) for t in types]): raise GMSOError("Types passed to DihedralType " "need to be strings corresponding to AtomType names") return types