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When you use the Output:Variable, set the time step to 'timestep', e.g., Output:Variable,*,Zone Mean Air Temperature,timestep;
Make sure the EnergyPlus and the Ptolemy are using the same time step, e.g., 600s per time step: In EnergyPlus, Timestep,6; In Ptolemy, SDF Diector, set period = 600 (or refer to a parameter), and set the iterations = number of total time steps.