/******************* NanorexUtility *******************
 ******************************************************/
/**
@defgroup NanorexUtility Nanorex Utility
	General-use classes.
 */

/******************* Logging *******************/
/**
@defgroup Logging Logging
	Simple logging mechanism.
	@ingroup NanorexUtility
 */

 
/******************* NanorexInterface *********************
 **********************************************************/
/**
@defgroup NanorexInterface Nanorex Interface
	Interface to Nanorex application cores.
 */

/******************* PluginArchitecture ********************/
/**
@defgroup PluginArchitecture Plugin Architecture
	Plugin architecture for extending the functionality of Nanorex applications.
	@ingroup NanorexInterface
	The following figure shows the relations between the main components of the simulator and highlights the plugin components.
	
	@image html soft-arch-overview.png
	
    - The NanoHive-1 Core and Physical Interaction Manager coordinate all components of the simulator
    - The Simulation Control plugins are used to configure, control, and monitor the simulation
    - The Entity Management plugin stores each molecule in the nano system being simulated and makes them available for calculation
    - The Data Import/Export plugins are used to import and export nano systems and nano devices
    - The Physical Interaction Calculators are the distributable layer of the simulator and perform the actual simulation calculations depending on which Physical Interaction plugins they have loaded
    - The Entity Traversal plugins provide ways for the Physical Interaction Manager to traverse through the simulation space and distribute the simulation across the Physical Interaction plugins
    - The Simulation Results plugins are invoked to provide the interim and final results of the simulation
 */


/******************* ChemistryDataModel *******************
 **********************************************************/
/**
@defgroup ChemistryDataModel Chemistry Data Model
	Data model for the storage of chemical structure data.
	@ingroup NanorexInterface
	The following figure shows the data model for cells in the simulation space. Internally, NanoHive-1 recursively divides the simulation space into cells, so at the top level, the simulation space is itself a cell. Physical Interaction plugins are passed cells (NH_Cell objects) for calculation.
	
	@image html cell-data-model.png
	
	- Each NH_Cell has a MeasurementSet.
	- All NH_Cell entities are accessed directly via unique integer identifier.
	- Each entity knows its child identifiers.
 */