Dimer coordinates

[psi-rking]

Going to get these usable.

• [x] Added test case that tests code that orients dimers with randomly created fragments, reference points, and weights. Works when you throw atoms and diatomics at it. Fixed acouple of related bugs in dimerfrag.py.
• [ ] Fix special case of polyatomic, linears. May defer. - Defered to separate issue.
• [x] Add test case that shows how to explictly do displacements with molecules.
• [x] Add example of PES scan using these coordinates.
• [x] Add optimization test case.

[codecov[bot]]

Codecov Report

Merging #48 into master will increase coverage by 10.00%. The diff coverage is 91.66%.

@@             Coverage Diff             @@
##           master      #48       +/-   ##
===========================================
+ Coverage   72.14%   82.14%   +10.00%     
===========================================
  Files          34       34               
  Lines        5331     5490      +159     
===========================================
+ Hits         3846     4510      +664     
+ Misses       1485      980      -505     

Impacted Files	Coverage Δ
optking/tors.py	94.73% <0.00%> (ø)
optking/optparams.py	65.15% <75.00%> (-0.09%)	:arrow_down:
optking/addIntcos.py	84.38% <83.67%> (+1.10%)	:arrow_up:
optking/frag.py	85.47% <86.66%> (-2.88%)	:arrow_down:
optking/displace.py	87.98% <88.46%> (-0.37%)	:arrow_down:
optking/dimerfrag.py	93.06% <93.75%> (+84.84%)	:arrow_up:
optking/__init__.py	100.00% <100.00%> (ø)
optking/molsys.py	92.69% <100.00%> (+8.62%)	:arrow_up:
optking/stepAlgorithms.py	90.00% <100.00%> (+0.04%)	:arrow_up:
optking/v3d.py	66.17% <100.00%> (+1.06%)	:arrow_up:
... and 12 more

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[psi-rking]

I guess I just disagree with standards on what is readable. Perhaps it is my older eyes, but when I see x = [(((d,d),(x),d))...] I just want to add spaces to better comprehend. so I think they sacrifice readability for the sake of consistency. However, I do not feel strongly about it, and it's fine with me if you would like to format check.

[psi-rking]

On the test case, I just created an issue about the need for test cases with linear monomers. Would only be ideal if fragments were either exactly linear by symmetry, or the user wants them to remain frozen. Both reasonably common cases.

[psi-rking]

But I moved that to a separate issue because I would like to get this merged.