Pulse simulator doc strings and changing naming of qubit_list

[DanPuzzuoli]

Summary

Closes #433
Closes #500

Adding doc strings for for pulse simulator files pulse_simulator.py, pulse_system_model.py, duffing_model_generators.py.

Changed qubit_list to subsystem_list in hamiltonian_model, pulse_system_model, and digest, and updated all relevant tests.

Details and comments

Changes are:

1. Added doc strings for relevant classes/functions in above mentioned files.
2. Updated aer __init__.py file to put relevant classes/methods in API doc generations: added PulseSimulator to the list of backends, and added a section called OpenPulse to have PulseSystemModel and duffing_model_generators.
3. Updated backends __init__.py file to import PulseSimulator.
4. Updated openpulse __init__.py file to import duffing_system_model and PulseSystemModel.
5. Removed warning for off-diagonal pieces of Hamiltonian from eigenvector re-ordering code in HamiltonianModel as it was going off in situations that it shouldn't, and updated related test to not check for the warning.
6. Changed qubit_list to subsystem_list and qubit_dims to subsystem_dims in all relevant places, and removed oscillator_dims from HamiltonianModel.

[chriseclectic]

LGTM.

I want to restructure some of the API docs a little bit (add the pulse models to their own section, not have them show up under the provider), but I will make a follow up PR to do this, along with a general cleanup of inits and paths in the pulse directory.