Added ability to run in containers.

Updated to the new infrastructure that supports running in containers.

Bugfix: properties that are constant

A property, such as the total energy, can be a constant over an MD run due to precision of the trajectory. This caused errors because the autocorrelation function is not defined. These cases are now detected and the ACF not calculated for them.

Bugfix in thermal conductivity

Corrected the names of input files and made them all similar to avoid future confusion.

Bugfix: correct reading final structures

Also added support for getting the final velocities and reusing them in subsequent steps.

Bugfix: not reading structure properly after dynamics

Merge pull request #45 from molssi-seamm/dev

Bugfix: not reading structure after dynamics.

Added support for tabulated angle potentials.

Merge pull request #44 from molssi-seamm/dev

Added support for tabulated angle potentials

Bugfix: error in x-axes of LAMMPS trajectory graphs

• The size of the x-axes of the trajectory graphs were wrong, often much too large, compressing the actual data near the beginning of the graph.
• Fixed an issue with systems with no non-bonds.

Bugfix: fixed more issues with heat flux and Class 2 forcefields.

• Avoided using centroid/stress/atom for heat flux in standard NVE, NVT, ... dynamics
  with Class 2 forcefield.
• Added option to not use centroid/stress/atom for any forcefield.

Bugfix: heat flux with Class 2 forcefields.

Avoided issue with centroid/stress/atom not working with Class 2 forcefields

Adding transport properties

• Added trajectory panel to support diffusion, viscosity and simple thermal
  conductivity.
• Added support for separate GPU versions of LAMMPS.
• Added support for command-line arguments to LAMMPS, mainly used for accelerators.
• Added support for using modules.