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Since some variables need to be defined as inputs in your EES model when coupled with TRNSYS, the actual EES code is different between a stand-alone EES project and one that is coupled with TRNSYS. It sounds like you have broken your EES code when defining which variables are to be inputs from TRNSYS. I would suggest going back to your stand-alone EES project and retry defining the inputs from TRNSYS. It may help to do this one variable at a time to make sure that everything is working.