To run the code, please insert run the line: sh run.sh to test your randomly initialized models. I am sorry for my low-tech code, when a pdb pop up on your screen, type x_cossim then write the value (to an excel file, for example). Then hit c (which means continue to the next layer). By doing that 12 times, which is the number of layers, you will get all the cossim similarity you need for all layers.
In case you want to load your trained model, please un-comment the line from 389 to 391 in the main.py.