Thank you Howard,
I ran into another issue with these simulations.
The BC behaves differently if I create a small model (1 period) vs if I create a full model and subtract the extra parts of the model to obtain 1 period of the motor. The flux distribution is wrong for the case where I am subtracting the masking rectangles from the full model. This is the only difference in the models. Everything else is same. Here are the pictures. Top picture has a smaller model. Bottom one is subtracted full model.
Thank you
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