Josephson junctions and junction arrays are well studied devices in superconductivity. With external magnetic fields one can modulate the phase in a long junction and create traveling, solitonic waves of magnetic flux, called fluxons. Today, it is also possible to device two different types of junctions: depending on the sign of the critical current density, they are called 0- or pi-junction. In turn, a 0-pi junction is formed by joining two of such junctions. As a result, one obtains a pinned Josephson vortex of fractional magnetic flux, at the 0-pi boundary. Here, we analyze this arrangement of superconducting junctions in the context of an atomic bosonic quantum gas, where two-state atoms in a double well trap are coupled in an analogous fashion. There, an all-optical 0-pi Josephson junction is created by the phase of a complex valued Rabi-frequency and we a derive a discrete four-mode model for this situation, which qualitatively resembles a semifluxon.
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