The paper presents a new method of structured encoding of global internal states and events in Reconfigurable Logic Controllers, which are directly mapped into Field Programmable Gate Arrays (FPGA). Modular, concurrently decomposed, colored state machine is chosen as a intermediate model, before the mapping of Petri net into an array structure of dedicated but very flexible and reliable digital system. The initial textual specification in formal Gentzen logic serves both as a design description for a rapid prototyping, as well as formal model, suitable for detailed computer-based reasoning about optimized and synthesized logic controller, implemented in configurable hardware. Only the selected linear subset from general, universal propositional Gentzen Logic is necessary to deduce several properties of the net, such as relations of nonconcurrency among structurally ordered macroplaces. The goal of this paper is to present the design methodology for modeling and synthesis of discrete controllers using related Petri net theory, rule-based theory (mathematical logic), and VHDL
