Three-dimensional transport models are extensively used for simulations of passive (=non-reactive) tracer transport and for modeling the chemistry and transport of trace gases, which play a role in the photo and sulfur chemistry of the (global) troposphere. A general name for these models is a global circulation model (GCM).
When a GCM calculates its own wind fields it is called an on-line GCM. When the winds are taken from a weather prediction or a climate model, it is called an off-line GCM. A climate model is a model that calculates the climate and not necessarily the observed state of the atmosphere. A weather prediction model tries to forecast the state of the atmosphere by assimilation of observables (temperature, wind, ...) in the model.