Manages the decomposition of the simulation volume over MPI ranks to try to distribute work evenly with minimal communication overheads.
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file | atomdistribution.h |
| Declares the AtomDistribution struct.
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file | box.cpp |
| This file defines functions used by the domdec module for (bounding) box and pbc information generation.
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file | box.h |
| This file declares functions used by the domdec module for (bounding) box and pbc information generation.
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file | builder.h |
| This file declares a builder class for the manager of domain decomposition.
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file | cellsizes.h |
| Declares DD cell-size related functions.
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file | collect.h |
| Declares functions to collect state data to the master rank.
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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.
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file | computemultibodycutoffs.h |
| This file declares the function for computing the required cutoff distance for inter-domain multi-body interactions, when those exist.
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file | distribute.h |
| Declares the atom distribution function.
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file | dlb.cpp |
| This file implements functions to interact with the dynamic load balancing machinery.
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file | dlb.h |
| This file declares functions to interact with the dynamic load balancing machinery.
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file | dlbtiming.h |
| This file declares functions for timing the load imbalance due to domain decomposition.
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file | domdec.h |
| This file declares functions for mdrun to call to manage the details of its domain decomposition.
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file | domdec_constraints.cpp |
| This file implements functions for domdec to use while managing inter-atomic constraints.
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file | domdec_constraints.h |
| This file declares functions for domdec to use while managing inter-atomic constraints.
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file | domdec_internal.h |
| Declares implementation functions and types for the domain decomposition module.
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file | domdec_network.cpp |
| This file defines functions for (mostly) the domdec module to use MPI functionality.
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file | domdec_network.h |
| This file declares functions for (mostly) the domdec module to use MPI functionality.
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file | domdec_setup.cpp |
| This file defines functions used by the domdec module in its initial setup phase.
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file | domdec_setup.h |
| Declares functions for choosing the DD grid setup.
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file | domdec_specatomcomm.cpp |
| This file implements functions for domdec to use while managing inter-atomic constraints.
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file | domdec_specatomcomm.h |
| This file declares functions for domdec to use while managing communication of atoms required for special purposes.
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file | domdec_struct.h |
| Declares structures related to domain decomposition.
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file | domdec_vsite.cpp |
| This file implements functions for domdec to use while managing inter-atomic constraints.
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file | domdec_vsite.h |
| This file declares functions for domdec to use while managing virtual sites.
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file | dump.cpp |
| This file definees functions for DD to write PDB files e.g. when reporting problems.
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file | dump.h |
| This file declares functions for DD to write PDB files e.g. when reporting problems.
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file | ga2la.cpp |
| Implements functions for mapping from global to local atom indices.
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file | ga2la.h |
| Defines structures and functions for mapping from global to local atom indices. The functions are performance critical and should be inlined.
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file | gpuhaloexchange.h |
| Declaration of GPU halo exchange.
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file | gpuhaloexchange_impl.cpp |
| May be used to implement Domdec CUDA interfaces for non-GPU builds.
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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.
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file | localatomset.cpp |
| Implements classes in LocalAtomSet.h.
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file | localatomset.h |
| Declares gmx::LocalAtomSet.
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file | localatomsetdata.cpp |
| Declares gmx::internal::LocalAtomSetDataData.
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file | localatomsetdata.h |
| Declares gmx::internal::LocalAtomSetData.
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file | localatomsetmanager.cpp |
| Implements classes in LocalAtomSetmanager.h.
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file | localatomsetmanager.h |
| Declares gmx::LocalAtomSetManager.
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file | localtopology.cpp |
| This file defines functions used by the domdec module while building topologies local to a domain.
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file | localtopology.h |
| This file makes declarations used for building the local topology.
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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.
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file | localtopologychecker.h |
| This file declares functionality for checking whether local topologies describe all bonded interactions.
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file | makebondedlinks.cpp |
| Defines a function that makes the list of links between atoms connected by bonded interactions.
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file | makebondedlinks.h |
| Declares a function that makes the list of links between atoms connected by bonded interactions.
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file | mdsetup.h |
| Contains functions relevant to simulation setup in MD drivers.
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file | options.h |
| This file declares command-line options for mdrun related to domain decomposition.
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file | partition.cpp |
| This file defines functions for mdrun to call to make a new domain decomposition, and check it.
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file | partition.h |
| This file declares functions for mdrun to call to make a new domain decomposition, and check it.
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file | redistribute.h |
| Declares the atom redistribution function.
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file | reversetopology.cpp |
| This file defines functions used in making the reverse topology.
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file | reversetopology.h |
| This file makes declarations used for building the reverse topology.
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file | haloexchange_mpi.cpp |
| Tests for the halo exchange.
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file | hashedmap.cpp |
| Tests for the HashedMap class.
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file | localatomsetmanager.cpp |
| Tests for general functionality in gmx::LocalAtomSetManager and gmx::LocalAtomSet, which is only accesible through the manager.
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file | utility.cpp |
| Declares utility functions used in the domain decomposition module.
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file | utility.h |
| Declares utility functions used in the domain decomposition module.
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