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Best estimate system thermal-hydraulic codes in the nuclear engineering community, e.g., TRACE, RELAP3D, CATHARE-3, etc., were extended with 3D coarse-mesh components to better describe the 3D Thermal-Hydraulic (TH) phenomena taking place within the Reactor Pressure Vessel (RPV) and the core. The RPV is usually shaped like a cylinder while the core is mostly a cube. Hence, the TRACE code is equipped with a Cylindrical VESSEL and a Cartesian VESSEL. The former one is to represent the RPV (including core), pressurizer, and steam generator. The latter one is more appropriate to represent the core. The two components are connected by two Vessel-Junctions (VJ) at the core inlet and outlet. Due to the different nodalization between the two VESSELs, the analyst needs to do repetitive and error-prone work defining the cell-to-cell junctions and their TH parameters. To facilitate this process, the Karlsruhe Institute of Technology (KIT) has developed an automatic approach based on a mesh-constructing and field-mapping library, namely the MEDCoupling. These new capabilities of TRACE are demonstrated by the analysis of the coolant mixing for an academic case and the AP1000 reactor.