Draft: Basic MDI Communications

Establish <ENERGY and >COORDS commands in the MDI-yucca interface.

MDI commands will be implemented such that yucca will run "normally" once, then pause and wait for commands from a driver prior to termination.

The >COORDS command will update atomic position coordinates from the driver.

The <ENERGY command will re-run the last method stage of the input file, and return the state-averaged energy to the driver.

To-Do List:

• Initialize MDI communication in main.cpp
  • Make it so yucca can take -mdi command-line arguments
  • Add conditionals such that yucca runs as normal when no MDI options are passed in
• Set up an MDI node in main.cpp
  • Set up the run_mdi() in util/mdi_interface.cpp
  • Establish that the basic @DEFAULT and EXIT commands are properly implemented with MDI mechanic
• Set up the <ENERGY command to check for updated coordinates and re-run most recent Method_ class
  • Use MDI mechanic to verify basic implementation (MDI is receiving something from yucca)
  • Set up a mini MDI driver to test that MDI is receiving the right energy value from yucca
  • Expand <ENERGY command to re-run most recent Method_ class
• Set up the >COORDS command to modify the Geometry_ class
  • Use MDI mechanic to verify basic implementation (MDI is receiving something with the right data type/shape from yucca)
  • Set up a mini MDI driver to test that yucca is correctly changing the coordinates and producing the proper energy values for all methods

This addresses Task B of Issue #3