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/******************* 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.
*/
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