We propose a scheme for the initialization of a quantum computer based on
neutral atoms trapped in an optical lattice with large lattice constant. Our
focus is the development of a compacting scheme to prepare a perfect optical
lattice of simple orthorhombic structure with unit occupancy. Compacting is
accomplished by sequential application of two types of operations: a flip
operator that changes the internal state of the atoms, and a shift operator
that moves them along the lattice principal axis. We propose physical
mechanisms for realization of these operations and we study the effects of
motional heating of the atoms. We carry out an analysis of the complexity of
the compacting scheme and show that it scales linearly with the number of
lattice sites per row of the lattice, thus showing good scaling behavior with
the size of the quantum computer.