make topology independent of entity handle to make more

modules/mol/mm/examples/ethanol_example_using_topology.py

modules/mol/mm/examples/gb_example.py

modules/mol/mm/examples/gb_example_traj.dcd

modules/mol/mm/examples/gb_example_view_trajectory.py

modules/mol/mm/pymod/export_simulation.cc

modules/mol/mm/pymod/export_topology.cc

modules/mol/mm/src/mm_observer.cc

modules/mol/mm/src/mm_observer.hh

modules/mol/mm/src/simulation.cc

modules/mol/mm/src/simulation.hh

modules/mol/mm/src/topology.cc

modules/mol/mm/src/topology.hh

modules/mol/mm/src/topology_creator.cc

modules/mol/mm/src/topology_creator.hh

modules/mol/mm/tests/test_simulation.cc

modules/mol/mm/tests/test_topology.cc