  Controlling the phases of matter is a challenge that spans from condensed
materials to biological systems. Here, by imposing a geometric boundary
condition, we study controlled collective motion of Escherichia coli bacteria.
A circular microwell isolates a rectified vortex from disordered vortices
masked in bulk. For a doublet of microwells, two vortices emerge but their
spinning directions show transition from parallel to anti-parallel. A
Vicsek-like model for confined self-propelled particles gives the point where
two spinning patterns occur in equal probability and one geometric quantity
governs the transition as seen in experiments. This mechanism shapes rich
patterns including chiral configurations in a quadruplet of microwells, thus
revealing a design principle of active vortices.
