Utility functions in pyMBE should support hydrogels

Currently, some of the utility functions in pyMBE do not support hydrogels:
- [ ] `create_counterions`
- [ ] `get_particle_id_map`
- [ ] `calculate_net_charge`
- [ ] `calculate_HH`
- [ ] `get_particle_id_map`

The core problem is `get_particle_id_map`, because all other utility functions rely on it. 
