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Identical output in both control and experimental cases ( CLM4)

Hello,I have a question about having the same model output regardless of what type of case is run - control or experimental.For the control case I ran CLM4 for 2 years without changing any input datasets. For the experimental run a part of wetland landunits was replaced by vegetated ones ( crops). At this point I met a  'mismatch of input dimension' error.  A restart file created as a result of running an experimental case with blank finitdat string and subsequent run with this new restart file seemed to be working in terms of giving output. However, it turned out that the model outputs are exactly the same in both control and experimental runs even though the percentage of wetlands and vegetated areas was changed in the second case. Are there any suggestions on how to overcome this problem? Thanks in advance! 
 
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