domdec Directory Reference

Directory dependency graph for domdec:

Directories
directory	tests

Files
file	atomdistribution.cpp
file	atomdistribution.h
	Declares the AtomDistribution struct.
file	box.cpp
	This file defines functions used by the domdec module for (bounding) box and pbc information generation.
file	box.h
	This file declares functions used by the domdec module for (bounding) box and pbc information generation.
file	builder.h
	This file declares a builder class for the manager of domain decomposition.
file	cellsizes.cpp
file	cellsizes.h
	Declares DD cell-size related functions.
file	collect.cpp
file	collect.h
	Declares functions to collect state data to the main rank.
file	computemultibodycutoffs.cpp
	This file defines functions used by the domdec module while managing the construction, use and error checking for topologies local to a DD 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	distribute.cpp
file	distribute.h
	Declares the atom distribution function.
file	dlb.cpp
	This file implements functions to interact with the dynamic load balancing machinery.
file	dlb.h
	This file declares functions to interact with the dynamic load balancing machinery.
file	dlbtiming.cpp
file	dlbtiming.h
	This file declares functions for timing the load imbalance due to domain decomposition.
file	domainpaircomm.cpp
	Implements the DomainPairComm, DomainCommBackward and DomainCommForward classes.
file	domainpaircomm.h
	Declares classes for communication between domain pairs in the halo.
file	domdec.cpp
file	domdec.h
	This file declares functions for mdrun to call to manage the details of its domain decomposition.
file	domdec_constraints.cpp
	This file implements functions for domdec to use while managing inter-atomic constraints.
file	domdec_constraints.h
	This file declares functions for domdec to use while managing inter-atomic constraints.
file	domdec_internal.h
	Declares implementation functions and types for the domain decomposition module.
file	domdec_network.cpp
	This file defines functions for (mostly) the domdec module to use MPI functionality.
file	domdec_network.h
	This file declares functions for (mostly) the domdec module to use MPI functionality.
file	domdec_setup.cpp
	This file defines functions used by the domdec module in its initial setup phase.
file	domdec_setup.h
	Declares functions for choosing the DD grid setup.
file	domdec_specatomcomm.cpp
	This file implements functions for domdec to use while managing inter-atomic constraints.
file	domdec_specatomcomm.h
	This file declares functions for domdec to use while managing communication of atoms required for special purposes.
file	domdec_struct.h
	Declares structures related to domain decomposition.
file	domdec_vsite.cpp
	This file implements functions for domdec to use while managing inter-atomic constraints.
file	domdec_vsite.h
	This file declares functions for domdec to use while managing virtual sites.
file	domdec_zones.cpp
	Implements the DomdecZones class.
file	domdec_zones.h
	Declares the DomdecZones class and helper structs.
file	dump.cpp
	This file definees functions for DD to write PDB files e.g. when reporting problems.
file	dump.h
	This file declares functions for DD to write PDB files e.g. when reporting problems.
file	ga2la.cpp
	Implements functions for mapping from global to local atom indices.
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	gpuhaloexchange_impl.cpp
	May be used to implement Domdec CUDA interfaces for non-GPU builds.
file	gpuhaloexchange_impl_gpu.cpp
	Implements shared code for GPU halo exchange.
file	gpuhaloexchange_impl_gpu.h
	Declares the implementation of GPU Halo Exchange.
file	gpuhaloexchange_impl_gpu_sycl.cpp
	Implements GPU halo exchange using SYCL.
file	haloexchange.cpp
	Implements the HaloExchange class for halo communication of coordinates and forces.
file	haloexchange.h
	Declares the HaloExchange class for halo communication of coordinates and forces.
file	haloexchangesetup.cpp
	Implements the setup() method for the HaloCommunication class.
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.cpp
	Implements classes in LocalAtomSet.h.
file	localatomset.h
	Declares gmx::LocalAtomSet.
file	localatomsetdata.cpp
	Declares gmx::internal::LocalAtomSetDataData.
file	localatomsetdata.h
	Declares gmx::internal::LocalAtomSetData.
file	localatomsetmanager.cpp
	Implements classes in LocalAtomSetmanager.h.
file	localatomsetmanager.h
	Declares gmx::LocalAtomSetManager.
file	localtopology.cpp
	This file defines functions used by the domdec module while building topologies local to a domain.
file	localtopology.h
	This file makes declarations used for building the local topology.
file	localtopologychecker.cpp
	This file defines functions used by the domdec module while managing the construction, use and error checking for topologies local to a DD rank.
file	localtopologychecker.h
	This file declares functionality for checking whether local topologies describe all bonded interactions.
file	makebondedlinks.cpp
	Defines a function that makes the list of links between atoms connected by bonded interactions.
file	makebondedlinks.h
	Declares a function that makes the list of links between atoms connected by bonded interactions.
file	mdsetup.cpp
file	mdsetup.h
	Contains functions relevant to simulation setup in MD drivers.
file	nsgrid.cpp
file	nsgrid.h
file	options.h
	This file declares command-line options for mdrun related to domain decomposition.
file	partition.cpp
	This file defines functions for mdrun to call to make a new domain decomposition, and check it.
file	partition.h
	This file declares functions for mdrun to call to make a new domain decomposition, and check it.
file	redistribute.cpp
file	redistribute.h
	Declares the atom redistribution function.
file	reversetopology.cpp
	This file defines functions used in making the reverse topology.
file	reversetopology.h
	This file makes declarations used for building the reverse topology.
file	utility.cpp
	Declares utility functions used in the domain decomposition module.
file	utility.h
	Declares utility functions used in the domain decomposition module.