1. A method of changing layout of a semiconductor device, comprising the steps of: a) preparing a physical layout representative of a layout of circuit constituents of a semiconductor device to be realized with use of a Levenson type phase shift mask; b) detecting a contradictory area in the layout not conforming with predetermined design rules, said rules including rules for a same phase and rules for a reverse phase; c) converting the physical layout into a graphical representation including: c-1) detecting nodes and branches interconnecting the detected nodes from the physical layout, where each node represents a circuit element, a contact outside of the circuit element, a branching point of a wiring layer, or a terminal point of a wiring layer; c-2) converting the nodes and the branches into the graphical representation; d) solving the contradictory area in the graphical representation; and e) converting the graphical representation into a new physical representation.