Our BIBLE. Here you can check the sequence of function calls.

loop over N timesteps:
ev_set()
fix->initial_integrate()
fix->post_integrate()
nflag = neighbor->decide()
if nflag:
fix->pre_exchange()
domain->pbc()
domain->reset_box()
comm->setup()
neighbor->setup_bins()
comm->exchange()
comm->borders()
fix->pre_neighbor()
neighbor->build()
else
comm->forward_comm()
force_clear()
fix->pre_force()
pair->compute()
bond->compute()
angle->compute()
dihedral->compute()
improper->compute()
kspace->compute()
comm->reverse_comm()
fix->post_force()
fix->final_integrate()
fix->end_of_step()
if any output on this step: output->write()