Migrate to hoomd v4

[marjanalbooyeh]

This PR upgrades the hoomd version to 4.1 and updates the Simulation class based on the changed on HOOMD 4.

The main changes are around setting up the integrator methods and thermostats.

Basically, in HOOMD v4 NVT and NVE methods are replaced with hoomd.md.methods.ConstantVolume and NPT method is replaced with hoomd.md.methods.ConstantPressure.
In methods with constant a T, a thermostat needs to added from `hoomd.md.methods.thermostats".

Hoomd documentation for migrating to V4: https://hoomd-blue.readthedocs.io/en/v4.1.0/migrating.html#migrating-to-hoomd-v4

I still need to add some unit tests for thermostat setter.

[codecov]

Codecov Report

Merging #54 (33b5a8f) into main (98e2193) will decrease coverage by 0.20%.
The diff coverage is 82.60%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #54      +/-   ##
==========================================
- Coverage   93.88%   93.69%   -0.20%     
==========================================
  Files          18       18              
  Lines        1357     1379      +22     
==========================================
+ Hits         1274     1292      +18     
- Misses         83       87       +4     

Files Changed	Coverage Δ
hoomd_organics/library/simulations/tensile.py	100.00% <ø> (ø)
hoomd_organics/base/simulation.py	91.26% <76.47%> (-0.80%)	⬇️
hoomd_organics/utils/__init__.py	100.00% <100.00%> (ø)
hoomd_organics/utils/base_types.py	100.00% <100.00%> (ø)

[chrisjonesBSU]

Looks good so far! I like how you implemented the changes :)

I left a couple comments.

[chrisjonesBSU]

LGTM, Thanks!

We might just need a couple unit tests that check the new attributes and methods added, but after that this should be good to go :)