Hi Kai Chang,
From the link-to-system model, we can obtain the throughput as follows:
1) The subcarrier (post-equalization) SINR vector is obtained from the Link Quality Model.
2) In the Link Performance Model, this vector is compressed into a single effective SINR
3) This effective SINR is mapped into a single BLER by AWGN SNR-to-BLER curves from link level simulation.
4) This BLER is combined with the TB size resulting in the throughput.
For the calculation in the Vienna simulator, we can check the function calculate_final_average_throughput_Mbps in ueTrace.m
I hope this can help.