A scheme is presented to perform an entangling gate between two atomic ensembles or Bose-Einstein condensates in a optical cavity with a common optical mode. The method involves using a generalized Stimulated Raman Adiabatic Passage (STIRAP) to adiabatically evolve the ground state. We show that dark states exist for any atom number within the cavities, and find that the operation produces an unusual type of evolution where the minimum of the number of atoms between two levels transitions to another state. This produces a unconventional type of entangling Hamiltonian which creates a phase depending on the minimum operation. We analyze its reliability under a variety of conditions ranging from the ideal decoherence-free case to that including photon loss and spontaneous emission. Ways of combating decoherence are analyzed and the amount of entanglement that is generated is calculated.
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