The purpose of the article is to develop a refined methodology for the general design of a container terminal. The difference between the proposed design methodology and the existing ones is that a solution is proposed to change its throughput (annual container flow passing through it), without changing the dimensions of the container yard and the way containers are stored, that is, with the same capacity of the container yard. Such cases occur, for example, when it is necessary to reconstruct a container terminal. Cargo terminals for containers are a specific area of logistics and cargo delivery systems, where cargo is processed in consolidated transport modules – containers. The main stages of analyzing or projecting a warehouse as a complex stochastic technical system should be considered: objective setting (it should be single); selection and determination of elements of technological areas and warehouse structure, as various connections between system elements; analyzing of system functioning (including its simulation); consideration of system interaction with surrounding environment; consideration of results of the warehouse system performance, and operation. It is interesting to point out that this general methodology can be used while creating or analyzing any other transformation of technical or social system, which receives a flow of some objects with one set of parameters, processes it through its structure, and gives them out with other values of parameters. 
 This method of formalizing the functioning of the container terminal can be used for its calculations, modeling, research and optimization. In the processes of interaction with environmental systems, the container terminal passes from one state to another, which are characterized by the types and volume of technological operations that must be performed at the moment, cargo that must be stored, delivered to and from the terminal, assembled, sorted, business employee processes, forklifts, cranes and other equipment in use. The functioning of the container terminal (part of the warehouse system) as a procedure of transitions from one state to another can be represented in the form of a graph or transition probability matrix.
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