Interactions between lists of particles

Collaboration diagram for Interactions between lists of particles:

Description

Handles computing energies and forces for listed interactions.

Located here is the code for

• computing energies and forces for interactions between a small number of particles, e.g bonds, position restraints and listed non-bonded interactions (e.g. 1-4).
• high-level functions used by mdrun for computing a set of such quantities
• managing thread-wise decomposition, thread-local buffer output, and reduction of output data across threads.

Author

Mark Abraham mark..nosp@m.j.ab.nosp@m.raham.nosp@m.@gma.nosp@m.il.co.nosp@m.m

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

Files
file	bonded.cpp
	This file defines low-level functions necessary for computing energies and forces for listed interactions.
file	bonded.h
	This file contains declarations necessary for low-level functions for computing energies and forces for bonded interactions.
file	disre.h
	Declares functions for handling distance restraints.
file	listed_forces.cpp
	This file defines high-level functions for mdrun to compute energies and forces for listed interactions.
file	listed_forces.h
	This file contains declarations of high-level functions used by mdrun to compute energies and forces for listed interactions.
file	listed_forces_gpu.h
	This file contains declarations of high-level functions used by mdrun to compute energies and forces for listed interactions.
file	listed_forces_gpu_impl.cpp
	Implements GPU bonded lists for non-GPU builds.
file	listed_forces_gpu_impl.h
	Declares GPU implementation class for GPU bonded interactions.
file	listed_forces_gpu_impl_gpu.cpp
	Implements helper functions for GPU listed forces (bonded)
file	listed_forces_gpu_internal_sycl.cpp
	Implements SYCL bonded functionality.
file	listed_internal.cpp
	This file defines functions needed internally by the module.
file	listed_internal.h
	This file contains declarations for functions needed internally by the module.
file	manage_threading.cpp
	This file defines functions for managing threading of listed interactions.
file	manage_threading.h
	Declares functions for managing threading of listed forces.
file	orires.h
	Declares functions for handling orientation restraints.
file	pairs.cpp
	This file defines functions for "pair" interactions (i.e. listed non-bonded interactions, e.g. 1-4 interactions)
file	pairs.h
	This file declares functions for "pair" interactions (i.e. listed non-bonded interactions, e.g. 1-4 interactions)
file	position_restraints.cpp
	This file defines low-level functions necessary for computing energies and forces for position restraints.
file	position_restraints.h
	This file contains declarations necessary for low-level functions for computing energies and forces for position restraints.
file	restcbt.cpp
	This file contains function definitions necessary for computations of forces due to restricted angle, restricted dihedral and combined bending-torsion potentials.
file	restcbt.h
	This file contains function declarations necessary for computations of forces due to restricted angle, restricted dihedral and combined bending-torsion potentials.
file	bonded.cpp
	Implements test of bonded force routines.
file	pairs.cpp
	Implements test of 1-4 interactions.
file	position_restraints.cpp
	Implements position restraint tests.
file	utilities.h
	This file declares inline utility functionality.