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As far as the command line usage of EnergyPlus, you can provide files names for the simulation using the command line options described in the EnergyPlus Essentials document.
Concerning running a large set of simulations, several questions on the topic may be of use to you:
https://unmethours.com/question/11298/what-do-you-recommend-for-doing-parametric-simulations-in-e/
https://unmethours.com/question/4668/script-for-multiple-simulations/