Simulation input tools

[eirrgang]

This umbrella "enhancement" issue is to organize various tasks related to inspecting and setting simulation inputs with stand-alone tools and as data flow operations.

Tools and core functionality:

• Read MD parameters from TPR: TPR file reader #192
• write new TPR file with modified contents from user: Tool to update TPR #86
• write new TPR with modified contents from checkpoint file: Allow Context to automatically manipulate simulation input files to restore MD operation to a known state. #71
• generate TPR data from inputs other than existing TPR (e.g. grompp)
• abstractly produce simulation input objects (make_input())
• insert graph node to transform simulation input from one source to simulation input with modified parameters (most simple, a new tpr file with updated parameters for the simulation node) (e.g. modify_input()): Modify simulation parameter #85
• finish mapping the remaining parameters from TPR file reader #192

Along the way, encapsulation will lead to a distinction between file data and data flow abstractions.

• Add TPR file class to gmx.core
• Add checkpoint file awareness to gmx.core
• Add "simulationState" abstraction to gmx.core to capture full simulator state restored from checkpoint files, including configuration, topology, parameters, and numerical state with hysteresis.
• Read data and metadata (e.g. current step) from simulation state Allow Context to inspect GROMACS checkpoint files to determine timestep. #70, Session and client need access to trajectory step #56
• Map simulation state handle to simulation input (a single (or packaged) tagged artifact in the data flow)

In the near term, C++ classes map fairly directly to TPX inputs and outputs.

Commit ae15738 added gmx.core.copy_tprfile with an argument to set the nsteps in the new TPR file to end_time, which is kind of clunky.

To do: update and incorporate issues from #56 into more granular tasks and close #56