add write_at_start parameters to run functions

[chrisjonesBSU]

This is a quick PR that adds a parameter to the run functions called write_at_start This is the same parameter that is in hoomd.Simulation.run(), we're just passing along the parameter. One difference is that we change the default value from False to True

[codecov]

Codecov Report

Merging #46 (d25b69e) into main (15fd092) will not change coverage.
The diff coverage is 100.00%.

Additional details and impacted files

@@           Coverage Diff           @@
##             main      #46   +/-   ##
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  Coverage   93.83%   93.83%           
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  Files          18       18           
  Lines        1347     1347           
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  Hits         1264     1264           
  Misses         83       83           

Files Changed	Coverage Δ
hoomd_organics/base/simulation.py	91.96% <100.00%> (ø)

[marjanalbooyeh]

LGTM