Use more intuitive names for procedures

src/pairs/code_gen/cgen.py

src/pairs/ir/arrays.py

src/pairs/ir/variables.py

src/pairs/sim/arrays.py

src/pairs/sim/cell_lists.py

src/pairs/sim/features.py

src/pairs/sim/neighbor_lists.py

src/pairs/sim/properties.py

src/pairs/sim/simulation.py

src/pairs/sim/variables.py