Collaboration diagram for Modules for simulation functionality:

Description

Modules used in running simulations with mdrun.

Modules
	Spatial domain decomposition (for parallelization over MPI)
	Manages the decomposition of the simulation volume over MPI ranks to try to distribute work evenly with minimal communication overheads.

	Ewald-family treatments of long-ranged forces
	Computes energies and forces for long-ranged interactions using the Ewald decomposition. Includes plain Ewald, PME, P3M for Coulomb, PME for Lennard-Jones, load-balancing for PME, and supporting code.

	Interactive molecular dynamics (IMD)
	Allows mdrun to interface with VMD via the interactive molecular dynamics (IMD) protocol.

	Interactions between lists of particles
	Handles computing energies and forces for listed interactions.

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

	The modular simulator
	The modular simulator improves extensibility, adds Monte Carlo capabilities, promotes data locality and communication via interfaces, supports multi-stepping integrators, and paves the way for some task parallelism.

	Short-range non-bonded interaction module
	Computes forces and energies for short-range pair-interactions based on the Verlet algorithm. The algorithm uses pair-lists generated at fixed intervals as well as various flavors of pair interaction kernels implemented for a wide range of CPU and GPU architectures.

	Non-bonded pair interactions
	Implements non-bonded pair interaction functionality for NxM atom clusters.

	"Computational Electrophysiology" position swapping (swap)
	Implements the "Computational Electrophysiology" protocol.

	Assigning simulation tasks to hardware (taskassignment)
	Provides code that manages assignment of simulation tasks to hardware.

	Implementation of mdrun
	This module contains code that implements mdrun.

	Integration test utilities
	Functionality for testing mdrun as a whole.