Source code for gmso.core.atom_type

"""Support non-bonded interactions between sites."""
import warnings
from typing import Optional, Set

import unyt as u

from gmso.core.parametric_potential import ParametricPotential
from gmso.utils._constants import UNIT_WARNING_STRING
from gmso.utils.expression import PotentialExpression
from gmso.utils.misc import (

    from pydantic.v1 import Field, validator
except ImportError:
    from pydantic import Field, validator

[docs] class AtomType(ParametricPotential): __base_doc__ = """A description of non-bonded interactions between sites. This is a subclass of the gmso.core.Potential superclass. AtomType represents an atom type and includes the functional form describing its interactions and, optionally, other properties such as mass and charge. This class inhereits from Potential, which stores the non-bonded interaction between atoms or sites. The functional form of the potential is stored as a `sympy` expression and the parameters, with units, are stored explicitly. """ mass_: Optional[u.unyt_array] = Field( 0.0 * u.gram / u.mol, description="The mass of the atom type" ) charge_: Optional[u.unyt_array] = Field( 0.0 * u.elementary_charge, description="The charge of the atom type" ) atomclass_: Optional[str] = Field( "", description="The class of the atomtype" ) doi_: Optional[str] = Field( "", description="Digital Object Identifier of publication where this atom type was introduced", ) overrides_: Optional[Set[str]] = Field( set(), description="Set of other atom types that this atom type overrides", ) definition_: Optional[str] = Field( "", description="SMARTS string defining this atom type" ) description_: Optional[str] = Field( "", description="Description for the AtomType" ) def __init__( self, name="AtomType", mass=0.0 * u.gram / u.mol, charge=0.0 * u.elementary_charge, expression=None, parameters=None, potential_expression=None, independent_variables=None, atomclass="", doi="", overrides=None, definition="", description="", tags=None, ): if overrides is None: overrides = set() super(AtomType, self).__init__( name=name, expression=expression, parameters=parameters, independent_variables=independent_variables, potential_expression=potential_expression, mass=mass, charge=charge, atomclass=atomclass, doi=doi, overrides=overrides, description=description, definition=definition, tags=tags, ) @property def charge(self): """Return the charge of the atom_type.""" return self.__dict__.get("charge_") @property def mass(self): """Return the mass of the atom_type.""" return self.__dict__.get("mass_") @property def atomclass(self): """Return the atomclass of the atom_type.""" return self.__dict__.get("atomclass_") @property def doi(self): """Return the doi of the atom_type.""" return self.__dict__.get("doi_") @property def overrides(self): """Return the overrides of the atom_type.""" return self.__dict__.get("overrides_") @property def description(self): """Return the description of the atom_type.""" return self.__dict__.get("description_") @property def definition(self): """Return the SMARTS string of the atom_type.""" return self.__dict__.get("definition_")
[docs] def clone(self, fast_copy=False): """Clone this AtomType, faster alternative to deepcopying.""" return AtomType( name=str(, tags=self.tags, expression=None, parameters=None, independent_variables=None, potential_expression=self.potential_expression_.clone(fast_copy), mass=u.unyt_quantity(self.mass_.value, self.mass_.units), charge=u.unyt_quantity(self.charge_.value, self.charge_.units), atomclass=self.atomclass_, doi=self.doi_, overrides=set(o for o in self.overrides_) if self.overrides_ else None, description=self.description_, definition=self.definition_, )
def __eq__(self, other): if other is self: return True if not isinstance(other, AtomType): return False return ( == and self.expression == other.expression and self.independent_variables == other.independent_variables and self.parameters.keys() == other.parameters.keys() and unyt_compare( self.parameters.values(), other.parameters.values() ) and self.charge == other.charge and self.atomclass == other.atomclass and self.mass == other.mass and self.doi == other.doi and self.overrides == other.overrides and self.definition == other.definition and self.description == other.description ) def _etree_attrib(self): attrib = super()._etree_attrib() if self.overrides == set(): attrib.pop("overrides") return attrib def __repr__(self): """Return a formatted representation of the atom type.""" desc = ( f"<{self.__class__.__name__} {},\n " f"expression: {self.expression},\n " f"id: {id(self)},\n " f"atomclass: {self.atomclass}>" ) return desc
[docs] @validator("mass_", pre=True) def validate_mass(cls, mass): """Check to see that a mass is a unyt array of the right dimension.""" default_mass_units = u.gram / u.mol if not isinstance(mass, u.unyt_array): warnings.warn(UNIT_WARNING_STRING.format("Masses", "g/mol")) mass *= u.gram / u.mol else: ensure_valid_dimensions(mass, default_mass_units) return mass
[docs] @validator("charge_", pre=True) def validate_charge(cls, charge): """Check to see that a charge is a unyt array of the right dimension.""" if not isinstance(charge, u.unyt_array): warnings.warn( UNIT_WARNING_STRING.format("Charges", "elementary charge") ) charge *= u.elementary_charge else: ensure_valid_dimensions(charge, u.elementary_charge) return charge
@staticmethod def _default_potential_expr(): return PotentialExpression( expression="4*epsilon*((sigma/r)**12 - (sigma/r)**6)", independent_variables={"r"}, parameters={ "sigma": 0.3 * u.nm, "epsilon": 0.3 * u.Unit("kJ"), }, )
[docs] class Config: """Pydantic configuration of the attributes for an atom_type.""" fields = { "mass_": "mass", "charge_": "charge", "atomclass_": "atomclass", "overrides_": "overrides", "doi_": "doi", "description_": "description", "definition_": "definition", } alias_to_fields = { "mass": "mass_", "charge": "charge_", "atomclass": "atomclass_", "overrides": "overrides_", "doi": "doi_", "description": "description_", "definition": "definition_", }