This PR is quite an overhaul. It wasn't planned this way, but ended up so due to timing.

4 major changes are introduced:

1. Non-cubic target volumes can be set.

This was needed to run certain system configurations, like crystalline system where the box length is one direction is similar to the length of a chain
This will also be a useful feature once we start dialing in the systems to perform welding on. We can increase surface area at the interface and go with a smaller depth

2. Tensile testing systems and simulations

Initializes tensile testing simulations in hoomd by stretching the box along an axis
Creates a new system.py class that is very similar to the Interface system. The idea is that the gsd file output from a welding simulation would be input here before running a tensile test simulation.

3. Initializing and running coarse-grained simulations

New coarse-grained simulations can be generated using the same system parameters and initialization schemes available for all atom and united atom systems.
Adds a function that creates the needed hoomd objects to run the coarse-grained simulation using table potentials

API Changes to the System and Initializer classes

After some feedback from Rainier, I tweaked the Initialize (now Initializer) class to be front-facing rather than only used behind the scenes by the System class.

Other changes

Faster system generation: When the monomer sequence along the backbone isn't random, we don't have to build a new polymer compound n times, rather we can build it once and clone afterwards.
Moved hoomd potential wall generation into it's own function. This was code being repated in both the anneal and quench functions, now it only lives in once place.

TODO

[ ] Unit tests for cg systems and simulations
[x] Fix environment files. Have -gpu, -cpu, -nohoomd

Codecov Report

Merging #56 (36dcadb) into master (b9fddaa) will decrease coverage by 13.13%. The diff coverage is 70.05%.

:exclamation: Current head 36dcadb differs from pull request most recent head 68b127b. Consider uploading reports for the commit 68b127b to get more accurate results

@@             Coverage Diff             @@
##           master      #56       +/-   ##
===========================================
- Coverage   94.75%   81.62%   -13.14%     
===========================================
  Files           6        6               
  Lines         477      653      +176     
===========================================
+ Hits          452      533       +81     
- Misses         25      120       +95

Impacted Files	Coverage Δ
uli_init/simulate.py	`75.00% <62.27%> (-19.45%)`	:arrow_down:
uli_init/system.py	`84.86% <76.64%> (-9.30%)`	:arrow_down:

cmelab / polybinder

Non-cubic volumes, Tensile Testing, Coarse-grained systems #56

Codecov Report