Add custom force module and otf helper functions; remove xyz logs

[jonpvandermause]

Closes #151 by giving users the option to give the OTF trainer a custom force module.

Closes #153 by adding velocity initialization helper functions to md.py and supercell construction helper functions to util.py.

Because of the various issues with the .xyz logs described in #127, these output files have been removed for now.

[codecov-io]

Codecov Report

❗ No coverage uploaded for pull request base (master@f396026). Click here to learn what that means.
The diff coverage is 42.1%.

@@            Coverage Diff            @@
##             master     #152   +/-   ##
=========================================
  Coverage          ?   58.36%           
=========================================
  Files             ?       31           
  Lines             ?     4813           
  Branches          ?        0           
=========================================
  Hits              ?     2809           
  Misses            ?     2004           
  Partials          ?        0

Impacted Files	Coverage Δ
flare/output.py	86.72% <100%> (ø)
flare/md.py	100% <100%> (ø)
flare/otf.py	93.79% <66.66%> (ø)
flare/util.py	65.21% <8.51%> (ø)

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