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We present a method for calculating chemical equilibria of general multiphase systems. The method is based on a stoichiometric approach, which uses Newton's method to solve a system of mass-balance and mass-action equations. A stabilisation procedure is developed to promote convergence of the calculation when a presupposed phase in the chemical system is absent in the equilibrium state. The formulation of the chemical equilibrium problem is developed by presuming no specific details of the involved phases and species. As a consequence, the method is flexible and general enough so that the calculation can be customised with a combination of thermodynamic models that are appropriate for the problem of interest. Finally, we show the use of the method to solve relevant geochemical equilibrium problems found in modelling of carbon storage in highly saline aquifers.