Dear fD_masonry, first of all, please understand ATENA is being developed for simulations of real structural behaviour using nonlinear analysis, not for design. Applying design assumptions into nonlinear FEM analysis frequently leads to an ill-conditioned equation system or other numerical problems. Please make sure the material properties you are using are withing reasonable ranges, e.g., the NLCem2 material model should have the ratio of tensile and compressive strength (fc/ft) of about 1:10-1:20. The recommended way is to generate the material settings using mean cube strength (or the nearest cocnrete class), and only adjust values which have been measured. Otherwise, it is very easy to end up with an inconsistent set (and problems with the analysis). Please read details about the material model in ATENA Theory to make sure you understand the parameter meaning and relations before doing larger modifications.
After making sure the material settings are reasonable, check the convergence, and if you still see values exceeding the material limits, please see ATENA Troubleshooting Manual, 2.1.21 The tensile (or compressive) stresses exceed the tensile (or compressive) strength or yield stress – what is wrong?