Change PairsSimulation class by PairsRuntime

runtime/boundary_weights.hpp

runtime/copper_fcc_lattice.hpp

runtime/dem_sc_grid.hpp

runtime/domain/ParticleDataHandling.hpp

runtime/domain/block_forest.hpp

runtime/pairs.cpp

runtime/pairs.hpp

runtime/read_from_file.hpp

runtime/stats.hpp

runtime/thermo.hpp

runtime/timing.hpp

runtime/vtk.hpp

src/pairs/code_gen/cgen.py