Update data files and initialize domain separately from particle data

data/minimd_setup_32x32x32.input

data/minimd_setup_32x32x32_onetype.input

data/minimd_setup_4x4x4_onetype.input

examples/dem.py

examples/lj.py

runtime/read_from_file.hpp

src/pairs/sim/domain.py

src/pairs/sim/grid.py

src/pairs/sim/read_from_file.py

src/pairs/sim/simulation.py