To clarify more,
cs_set_atom_vars2.cpp reads the spins_initial.dat file to initialize. The spins_initial.dat file is created from a previous simulation output.
After running a new simulation, when looking at the initial spin output file (spins-00000000.data), it matches spins_initial.dat file. However, the corresponding location of the spins do not match any more.
spins_initial.png is the plot of the previous simulation output that was used to make spins_initial.dat.
spins-00000000.png is the plot of the initial spin output of the new simulation.