The software uses electrochemical performance modeling, auxiliary losses such as pumpoing and shunt current losses, a bottom up cost model. Optimization is done with respec to flow rate to get the highest efficiency. Calculations are done at constant power as opposed to constant current. Various stack areas are investigated, with each area corresponding to diffent power density required to meet the power requirement. At a power density corresponding to a fixed stack area, differnt combinations of current density and stack voltage are possible. The current density during discharge at low SOC fixes the upper limit of current density for a fixed stack area. Varying the flow rate and the dimensions of the manifold to each stack and dimensions of the flow channels within each cell determine losses. An effective voltage for each SOC is determined after losses are accounted for. The stack costs are determined by the stack area, while energy costs by the effective voltage. Determining the costs for various stack areas guide the optimization of stack and energy costs. Balance of Plant optimization of pump sizing is done taking into pump costs as function of pumping power and the flow rate effect on electrochemical efficiency and pumping losses. The model optimizes the system for vaious power to energy ratio and various chemistries. The tool developed is also able to do spline interpolation to get polarization curves from input data. The one of a kind tool allows user interaction.