Add unit class to FlowerMD and allow using real units in Simulation runs

[marjanalbooyeh]

This PR introduces a new Unit class to FlowerMD, which contains commonly used units from unyt package.

With this change, all values with units in FlowerMD are formatted as value * flower.Units.<unit>. For example, a temperature in Kelvin is 300 * flowermd.Units.K.

This PR also makes the following changes to the interface of run functions in Simulation class:

• The variable kT is now temperature , which can handle both kT values (unitless) and temperature values with units.
• The n_steps variable is now called duration, which can be both a number (number of steps) or time length with units.

ToDo:

• Make same changes for pressure and add pressure units

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[marjanalbooyeh]

Couple of issues that we need to look into:

• Build workflow fails due to some mamba env error. This happens only for Ubuntu. I couldn't pinpoint the error, it seems to be __glibc version.
• Some tests are failing. In test_molecules.test_polymer_different_num_mol, looks like there's a key error with mbuild compound. this might be because of recent changes on mbuild side that we need to account for. I'll look into it more closely.
• A new error has showed up in coarse graining tutorials when we want to visualize the coarse grained compounds in jupyter nb. It's coming from the Grits's CG_Compound.visualize() but once I narrowed it down, the error initiates from mbuild clone in method called by grits. This clone method doesn't copy all CG_Compound attributes including atomistic which causes error here.
• We also need to discuss how we want to handle temperature ramps in simulation run functions. Right now, the assumption is that temperature is passed either as a float (i.e. kT) or a unit value (for example 200 * Units.k). But we also support Hoomd ramps that have two kT values in them. We need to manage the temperatures in the Ramp object similarly. My suggestion is to define a Ramp class for flowermd with similar methods for temperature check. Users can only use flowermd's Ramp if they want to use a ramp. Same argument with pressure ramps.

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Codecov Report

Attention: Patch coverage is 92.55814% with 16 lines in your changes missing coverage. Please review.

Project coverage is 95.04%. Comparing base (a600b73) to head (807fdea).
Report is 55 commits behind head on main.

Files with missing lines	Patch %	Lines
flowermd/base/simulation.py	87.71%	14 Missing ⚠️
flowermd/internal/utils.py	90.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #137      +/-   ##
==========================================
+ Coverage   94.77%   95.04%   +0.27%     
==========================================
  Files          26       27       +1     
  Lines        1970     2160     +190     
==========================================
+ Hits         1867     2053     +186     
- Misses        103      107       +4     

Files with missing lines	Coverage Δ
flowermd/__init__.py	100.00% <100.00%> (ø)
flowermd/base/system.py	92.55% <100.00%> (+0.16%)	⬆️
flowermd/internal/__init__.py	100.00% <100.00%> (ø)
flowermd/internal/exceptions.py	89.74% <100.00%> (ø)
flowermd/internal/units.py	100.00% <100.00%> (ø)
flowermd/library/simulations/tensile.py	100.00% <100.00%> (ø)
...lowermd/modules/surface_wetting/surface_wetting.py	94.78% <100.00%> (+0.04%)	⬆️
flowermd/utils/utils.py	93.47% <100.00%> (+0.14%)	⬆️
flowermd/internal/utils.py	93.75% <90.00%> (-6.25%)	⬇️
flowermd/base/simulation.py	93.76% <87.71%> (+1.74%)	⬆️