Topology
schemas.atomistic.topology.TopologySchema
¶
Bases: BaseModel, YamlIO
Information that specifies the physical atomistic system.
ff_atom_type: Annotated[list[str] | None, {cadence: ensemble, uuid: 'e34c0e1b-0eaa-4679-b060-3fcfe737aa15'}] = Field(default=None)
class-attribute
instance-attribute
¶
In the context of force fields used in molecular dynamics simulations, an "atom type" refers to a specific classification assigned to individual atoms within a molecular system based on certain characteristics. Atom types play a crucial role in defining the parameters and potential energy functions used to calculate forces and motions during a simulation.
Each atom in a molecular system is assigned a particular atom type, which is typically associated with a set of parameters defining its behavior. These parameters include values such as atomic mass, partial charges, van der Waals radii, and bond, angle, and dihedral force constants. The specific values for these parameters are determined based on experimental data and quantum mechanical calculations.
Cadence: ensemble
UUID: e34c0e1b-0eaa-4679-b060-3fcfe737aa15
ids_component: Annotated[list[str] | None, {cadence: molecule, uuid: cf39af62 - d372 - 4747 - a431 - cf2fa0c8e119}] = Field(default=None)
class-attribute
instance-attribute
¶
Relates ids_entity
to a fragment label for chemical components or species.
Labels could be WAT or h2o for water, MeOH for methanol, bz for benzene,
etc. There are no standardized labels for species.
Cadence: molecule
UUID: cf39af62-d372-4747-a431-cf2fa0c8e119
ids_entity: Annotated[list[int] | None, {cadence: molecule, uuid: 'b490f2db-548e-4c92-a71a-8222c041ca54'}] = Field(default=None)
class-attribute
instance-attribute
¶
A uniquely identifying integer specifying what atoms belong to which entities.
Entities can be a related set of atoms, molecules, or functional group.
For example, a water and methanol molecule could be [0, 0, 0, 1, 1, 1, 1, 1, 1].
Cadence: molecule
UUID: b490f2db-548e-4c92-a71a-8222c041ca54