Spatial domain decomposition (for parallelization over MPI)

Collaboration diagram for Spatial domain decomposition (for parallelization over MPI):

Description

Manages the decomposition of the simulation volume over MPI ranks to try to distribute work evenly with minimal communication overheads.

Todo:

Get domdec stuff out of mdtypes/commrec.h

Author

Berk Hess hess@.nosp@m.kth..nosp@m.se

Classes
class	gmx::LocalAtomSet
	A local atom set collects local, global and collective indices of the home atoms on a rank. The indices of the home atoms are automatically updated during domain decomposition, thus gmx::LocalAtomSet::localIndex enables iteration over local atoms properties like coordinates or forces. TODO: add a LocalAtomSet iterator. More...
class	gmx::LocalAtomSetManager
	Hands out handles to local atom set indices and triggers index recalculation for all sets upon domain decomposition if run in parallel. More...

Files
file	builder.h
	This file declares a builder class for the manager of domain decomposition.
file	collect.h
	Declares functions to collect state data to the main rank.
file	computemultibodycutoffs.h
	This file declares the function for computing the required cutoff distance for inter-domain multi-body interactions, when those exist.
file	dlb.h
	This file declares functions to interact with the dynamic load balancing machinery.
file	dlbtiming.h
	This file declares functions for timing the load imbalance due to domain decomposition.
file	domdec.h
	This file declares functions for mdrun to call to manage the details of its domain decomposition.
file	domdec_network.h
	This file declares functions for (mostly) the domdec module to use MPI functionality.
file	domdec_struct.h
	Declares structures related to domain decomposition.
file	ga2la.h
	Defines structures and functions for mapping from global to local atom indices. The functions are performance critical and should be inlined.
file	gpuhaloexchange.h
	Declaration of GPU halo exchange.
file	hashedmap.h
	Defines structures and functions for mapping from keys to entries indices using a hash table. The functions are performance critical and should be inlined.
file	localatomset.h
	Declares gmx::LocalAtomSet.
file	localatomsetmanager.h
	Declares gmx::LocalAtomSetManager.
file	localtopology.h
	This file makes declarations used for building the local topology.
file	localtopologychecker.h
	This file declares functionality for checking whether local topologies describe all bonded interactions.
file	makebondedlinks.h
	Declares a function that makes the list of links between atoms connected by bonded interactions.
file	mdsetup.h
	Contains functions relevant to simulation setup in MD drivers.
file	options.h
	This file declares command-line options for mdrun related to domain decomposition.
file	partition.h
	This file declares functions for mdrun to call to make a new domain decomposition, and check it.
file	reversetopology.h
	This file makes declarations used for building the reverse topology.