Create dynamics.py with Freud MSD functionality

[chrisjonesBSU]

This PR puts the MSD from GSD functionality that we have floating around in various notebooks and python files into a single location.

Also, I updated get_type_position to accept a list (or iterable) of atom types and return their positions as opposed to only accepting a single atom type. I think this will offer more flexibility.

Still needs unit tests and doc strings, but I figured I'd put it up here for others to comment on.

[codecov]

Codecov Report

Merging #9 (ae99f24) into master (a806ed7) will decrease coverage by 0.80%.
The diff coverage is 97.36%.

@@             Coverage Diff             @@
##            master       #9      +/-   ##
===========================================
- Coverage   100.00%   99.20%   -0.80%     
===========================================
  Files            3        4       +1     
  Lines           93      125      +32     
===========================================
+ Hits            93      124      +31     
- Misses           0        1       +1     

Impacted Files	Coverage Δ
cmeutils/structure.py	100.00% <ø> (ø)
cmeutils/dynamics.py	96.00% <96.00%> (ø)
cmeutils/__init__.py	100.00% <100.00%> (ø)
cmeutils/gsd_utils.py	100.00% <100.00%> (ø)

[gwenwhite]

One thing I noticed when testing this code is that from cmeutils import gsd_utils was providing the error:
ImportError: cannot import name 'gsd_utils' from 'cmeutils' (unknown location)

I was able to get rid of the error running this instead :
import cmeutils.cmeutils.gsd_utils

Otherwise, looks great!

[jennyfothergill]

@gwenwhite that issue might be caused when cmeutils is not installed. Do you still get the error after running

pip install .

in the root directory (the top level directory for cmeutils containing setup.py)

[chrisjonesBSU]

Question about this:

    if stop is None:
        stop = -1

We do the same thing in gsd_rdf. Wouldn't it make more sense (and be easier for someone reading the code) to make the default parameter -1 rather than None

[jennyfothergill]

We do the same thing in gsd_rdf. Wouldn't it make more sense (and be easier for someone reading the code) to make the default parameter -1 rather than None

yeah... why do we do that?? I'm with you--let's switch that.

[jennyfothergill]

LGTM! :) I was able to get a reasonable MSD from one of my planckton runs.

Because we usually have a shrink step at the beginning of our simulations, it might be cool to have some automated detection for where the box size is stable. I think it's not necessary to hold up this PR though.

Also, I really like all the changes you've added to incorporate images into our utils!