1. A method for managing behavior of a CAD model, comprising: receiving a geometric object and corresponding physical object, for the CAD model, in a data processing system, and receiving a corresponding user annotation that specifies a simulation behavior by associating the geometric object with the corresponding physical object, wherein the physical object describes physical qualities and behaviors of the corresponding geometric object, including at least one of movement, collisions, connections, mass, velocity, or force; executing function code in a behavior object by the data processing system, to determine required references of the behavior object, wherein the required references indicate one or more physical objects that are required for execution of the behavior object; receiving and storing an assignment of at least one of the required references of the behavior object to the physical object by the data processing system; storing the geometric object, physical object, and behavior object in the data processing system as associated with the CAD model; simulating operation of at least part of the CAD model by the data processing system according to the specified simulation behavior, including executing the behavior object by the data processing system to modify a state of the physical object.