I got it, the problem is that the real beam doesn't crack symmetrically, therefore different displacements occur under the loading points.
My first idea would be to model only one side of the beam assuming it behaves symmetrically. However, this is not your case. It probably happened due to random nature of concrete material, small inaccuracies in the experiment setup and other non controlled issues. Usually in this kind of experiments a small crack inducer is made so that first crack occurs in the midspan.
Of course you can make a pre-defined crack in the concrete beam as per the experiment results (not certain if such simulation can be considered as "pure", you'd better discuss it with your supervisor). Even though the beam cracks unsymmetrically in ATENA, I don't see any problem with the loading frame. You have to define only Z- contacts and restrict X-displacement.
I would highly recommend to start with 2D model because the result should be identical for that kind of problem but calculation time is much less. You can later create 3D model when you get adequate results from 2D model.
There is a sample FRC beam model in ATENA example folder. Just modify the model for your geometry, that's it.