After running the simulation, batteries operate more than fuel cells. I want to ask you why this has happened. For me, the only explanation is that because HOMER takes economical data into account and because batteries have lower initial as well as O&M costs than the fuel cells, they are more advantageous to operate.  Is this explanation correct or has HOMER been programmed to operate the components in a specific order?

That’s a great question.  You are right that HOMER takes costs into account when deciding how to operate the system.  It calculates the fixed and marginal cost of producing power from the fuel cell and displays that on the fuel cell tab of the Simulation Results window.  (That’s true of version 2.67.)  It also calculates the cost of discharging the battery, which is comprised of two parts:  the cost of wearing out the battery, and the cost of the energy that went into the battery.  Both of those appear on the battery tab of the Simulation Results window.

In each timestep, when the supply of renewable power is insufficient to serve the load and the system needs power from the battery or fuel cell, HOMER compares the cost of each, and uses the one that can supply the load (and operating reserve requirement) at the lowest cost.