A three-dimensional MHD solver is described in the paper. The solver simulates reacting flows with nonequilibrium between translational-rotational, vibrational and electron translational modes. Also included are models for electrical conductivity, electron thermal conductivity and collision frequencies. The conservation equations are discretized with implicit time marching and the second-order Steger-Warming scheme, and the resulted linear system is solved iteratively with a fully coupled parallel preconditioned GMRES method that is implemented by the PETSc package. The results of convergence tests are plotted, which show good scalability and convergence acceleration between two and Ave times when compared with the DPLR method. Then Ave test runs are conducted simulating the experiments done at the NASA Ames MHD channel, and the calculated pressures, temperatures, electrical conductivity, back EMF and now accelerations are shown to agree with the experimental data. A scramjet-driven Diagonal Conducting Wall MHD generator is also simulated which works at the design parameters of the HVEPS program taken from the reference paper. The scramjet model is taken from University of Queensland, and one set of their scramjet experiments is simulated with both fuel on and off. Then MHD power generation computation is performed on top of the scramjet model, and plotted are conductivity and Hall parameter distribution. The computed power generation is 2.2MW which is within the design power regime.