Diffusivity-step

* Fixed a bug where the data was not being correctly initialized if the step was in
a loop. This caused the timing results to be incorrect.
* Added actual number of samples for the MSD and length of the Helfand integral to
the results.

* Added an option to use the Yeh-Hummer hydrostatic correction for the effects of
the finite cell size. The viscosity is required as an input, but the correction
eliminates the need to extrapolate to 1/L = 0.
* Added control parameters and timings to the available results.

* Simplified error analysis to safe approach of analyzing the diffusion constants
over runs.
* Improved fitting of the curves to focus on the central linear portion. There are
reasonable defaults but the user can adjust as needed.
* Provided a combined average and error bars when both the MSF approach and Helfand
moments are used.
* Capture temperature, pressure, and cell size from the MD step, providing 1/L as a
result since the true diffusion constants are found by extrapolating to 1/L = 0.
* Provided control over the number of steps for the expensive numerical integration
in the Helfand moments, providing a reasonable default of 1000.

* Now fixed and seems to be working.

* Removed weighting of the fit by the stdev since it is too biased to the beginning
* Added control over the portion of the data to fit in order to avoid the initial
curvature and poor data towards the end.

* Fixed a bug where the options for the subflowchart were not being parsed
correctly.