Implementation of mdrun utility functionality

Collaboration diagram for Implementation of mdrun utility functionality:

Description

This module contains code that implements general infrastructure for mdrun that does not suit any other module.

Classes
class	gmx::MDModules
	Manages the collection of all modules used for mdrun. More...

Files
file	freeenergy.cpp
	Defines helper functions for mdrun pertaining to free energy calculations.
file	freeenergy.h
	Declares helper functions for mdrun pertaining to free energy calculations.
file	handlerestart.cpp
	This file declares functions for mdrun to call to manage the details of doing a restart (ie. reading checkpoints, appending output files).
file	handlerestart.h
	This file declares functions for mdrun to call to manage the details of doing a restart (ie. reading checkpoints, appending output files).
file	logging.cpp
	Implements the MD log file handling routines.
file	logging.h
	Declares the MD log file handling routines.
file	mdmodulesnotifier.h
	Declares gmx::MDModulesNotifier and builder.
file	mdmodulesnotifiers.cpp
	Implements routines in mdmodulesnotifiers.h.
file	mdmodulesnotifiers.h
	Declares gmx::MDModulesNotifiers.
file	multisim.cpp
	Implements the multi-simulation support routines.
file	multisim.h
	Declares the multi-simulation support routines.
file	printtime.h
	Declares functions that write timestamps to e.g. log files.
file	mdmodulesnotifier.cpp
	Tests MDModulesNotifier.
file	threadaffinity.h
	Declares functions for managing mdrun thread affinity.