The Lagrange multiplier method and the penalty method are the common methods when applying essential boundary conditions in meshless method. In order to compare the advantage and the disadvantage of two methods, the hybrid element-free Galerkin (HEFG) method was presented for analyzing 3D Helmholtz equation. By introducing the dimensional split method, the governing equation could be split into a few 2D forms, for every 2D problem, the Lagrange multiplier method and the penalty method were used to apply the boundary conditions, and the equivalent functional could be established, thus the corresponding integral weak forms could be derived. By introducing the improved moving least squares (IMLS) approximation to establish shape functions, the discrete equation of 2D forms could be obtained. In dimensional split direction, the finite difference method was selected to couple these 2D equations, thus the final discrete equation of 3D Helmholtz equation was obtained. In numerical examples, by comparing the computational accuracy and computational time of numerical results, the advantages and disadvantages of two methods for applying boundary conditions were analyzed, respectively. It is shown that the penalty method is better than the Lagrange multiplier method when applying essential boundary conditions.
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