Dear Bikip, there are 2 basic solutions with ATENA:
A. Include the previous phase when the cracks develop in your model. This usually gives the best results (if one manages to reproduce the pre-crack pattern reasonably).
B. Represent the pre-crack with Interface elements.
In your particular case, A. involves a volume with applied expansion (positive initial strain) representing the corroding reinforcement, or the reinforcement+some concrete volume around it (to keep element sizes comparable within the model).
If you are interested in more detailed advice, please follow ATENA Troubleshooting, 2.1.1 to send us sketches+explanation of your planned analysis.
Regards.