This method was governed by a variational principle applied to a certain function. The resulting variational relation was then treated by introducing some unknown multipliers in connection with constraint relations. After the elimination of these multipliers the generalized momenta were found to be certain functions of the partial derivatives of the Hamilton Jacobi function with respect to the generalized coordinates and the time. Then the partial differential equation of the classical Hamilton-Jacobi method was modified by inserting these functions for the generalized momenta in the Hamiltonian of the system.
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You can solve the system of equations with three variables using the substitute method, or using matrix operations.
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You would solve them in exactly the same way as you would solve linear equations with real coefficients. Whether you use substitution or elimination for pairs of equations, or matrix algebra for systems of equations depends on your requirements. But the methods remain the same.