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In applications of the Energy Finite Element Analysis (EFEA) there is an increasing need for developing comprehensive models with a large number of elements which include both structural and interior fluid elements, while certain parts of the structure are considered to be exposed to an external fluid loading. In order to accommodate efficient computations when using simulation models with a large number of elements, joints, and domains, a substructuring computational capability has been developed. The new algorithm is based on dividing the EFEA model into substructures with internal and interface degrees of freedom. The system of equations for each substructure is assembled and solved separately and the information is condensed to the interface degrees of freedom. The condensed systems of equations from each substructure are assembled in a reduced global system of equations. Once the global system of equations has been solved the solution for each substructure is pursued.