Add charmm_writer and change import in 3x3x1.0-3 nvt build

[rmatsum836]

Addresses #38.

[rmatsum836]

If this looks okay, we can go ahead and change the rest of the import statements to import charmm_writer from the utils directory.

[justinGilmer]

Looks good to me, havent tested heavily though.

Also, here is a one-liner to find all instances and replace, assuming you are in the top level of mosdef_slitpore. Note that this works with the sed program that ships with MacOS (BSD-flavored sed).

grep -rl "import mbuild.formats.charmm_writer as mf_charmm" .  | xargs sed -i '' -e 's/import\ mbuild\.formats\.charmm\_writer\ as\ mf\_charmm/from\ mosdef\_slitpore\.utils\ import\ charmm\_writer\ as\ mf\_charmm/'

Uses bash to just find the files where the pattern occurs, passes the file locations as arguments (thanks to xargs) to the sed command. Just verify the diff afterwards. It looks good on my side.