Module MdLib

Collaboration diagram for Module MdLib:

Description

A brief description for Module MdLib.

Files
file	boxdeformation.cpp
	Defines the box deformation code.
file	boxdeformation.h
	Declares interface to box deformation code.
file	broadcaststructs.h
	Convenience wrappers for broadcasting structs.
file	checkpointhandler.cpp
	Defines the checkpoint handler class.
file	checkpointhandler.h
	Declares the checkpoint handler class.
file	constr.cpp
	Defines the high-level constraint code.
file	constr.h
	Declares interface to constraint code.
file	energydrifttracker.cpp
	Implements functions from the EnergyDriftTracker class.
file	energydrifttracker.h
	Declares and defines the EnergyDriftTracker class.
file	energyoutput.cpp
	Defines code that writes energy-like quantities.
file	energyoutput.h
	Header for the code that writes energy-like quantities.
file	expanded_internal.cpp
	Implements internal functionality for expanded ensemble.
file	expanded_internal.h
	Declares internal functionality for expanded ensemble.
file	freeenergyparameters.h
	Handling of free energy parameters.
file	gpuforcereduction.h
	Declares the GPU Force Reduction.
file	gpuforcereduction_impl.cpp
	Implements backend-agnostic GPU Force Reduction functions.
file	gpuforcereduction_impl.h
	Declares the GPU Force Reduction.
file	gpuforcereduction_impl_internal.h
	Declares vendor-specific function to launch force reduction kernel.
file	gpuforcereduction_impl_internal_hip.cpp
	Implements GPU Force Reduction using HIP.
file	gpuforcereduction_impl_internal_sycl.cpp
	Implements GPU Force Reduction using SYCL.
file	gpuforcereduction_impl_stubs.cpp
	May be used to implement force reduction interfaces for non-GPU builds.
file	leapfrog_gpu.cpp
	Implements Leap-Frog using CUDA.
file	leapfrog_gpu.h
	Declarations for GPU implementation of Leap-Frog.
file	leapfrog_gpu_internal.h
	Declarations for backend specific GPU functions for Leap-Frog.
file	leapfrog_gpu_internal_hip.cpp
	Implements Leap-Frog using HIP.
file	leapfrog_gpu_internal_sycl.cpp
	Implements Leap-Frog using SYCL.
file	lincs.cpp
	Defines LINCS code.
file	lincs.h
	Declares interface to LINCS code.
file	lincs_gpu.cpp
	Implementations of LINCS GPU class.
file	lincs_gpu.h
	Declares the class for GPU implementation of LINCS.
file	lincs_gpu_internal.h
	Declare backend-specific LINCS GPU functions.
file	lincs_gpu_internal_hip.cpp
	Implements LINCS kernels using HIP.
file	lincs_gpu_internal_sycl.cpp
	Implements LINCS kernels using SYCL.
file	makeconstraints.h
	Declares and implements factory function for Constraints.
file	mdgraph_gpu.h
	Declares the MD Graph class.
file	mdgraph_gpu_impl.cpp
	May be used to implement MD graph CUDA interfaces for non-GPU builds.
file	mdgraph_gpu_impl.h
	Declares the MD Graph class.
file	mdgraph_gpu_impl_sycl.cpp
	Defines the MD Graph class.
file	resethandler.cpp
	Defines the reset handler class.
file	resethandler.h
	Declares the reset handler class.
file	settle.cpp
	Defines SETTLE code.
file	settle.h
	Declares interface to SETTLE code.
file	settle_gpu.cpp
	Implements SETTLE using GPU.
file	settle_gpu.h
	Declares class for GPU implementation of SETTLE.
file	settle_gpu_internal.h
	Declares backend-specific functions for GPU implementation of SETTLE.
file	settle_gpu_internal_hip.cpp
	HIP-specific routines for the GPU implementation of SETTLE constraints algorithm.
file	settle_gpu_internal_sycl.cpp
	SYCL-specific routines for the GPU implementation of SETTLE constraints algorithm.
file	shake.cpp
	Defines SHAKE code.
file	shake.h
	Declares interface to SHAKE code.
file	simulationsignal.cpp
	This file defines functions for inter- and intra-simulation signalling by mdrun.
file	simulationsignal.h
	This file declares functions for inter-rank signalling by mdrun.
file	stophandler.cpp
	Defines StopHandler, a helper class and two stop conditions.
file	stophandler.h
	Declares StopHandler, a helper class and two stop conditions.
file	constr.cpp
	SHAKE and LINCS tests.
file	constrtestdata.cpp
	SHAKE and LINCS tests.
file	constrtestdata.h
	SHAKE and LINCS tests header.
file	constrtestrunners.cpp
	Function to run SHAKE and LINCS on CPU.
file	constrtestrunners.h
	SHAKE and LINCS tests runners.
file	constrtestrunners_gpu.cpp
	Subroutines to run LINCS on GPU.
file	energydrifttracker.cpp
	Tests for the EnergyDriftTacker class.
file	energyoutput.cpp
	Tests for energy output to log and .edr files.
file	expanded.cpp
	Tests for expanded ensemble.
file	langevin.cpp
	Tests for the Leap-Frog integrator.
file	langevintestdata.cpp
	Defines the class to accumulate the data needed for the Langevin integrator tests.
file	langevintestdata.h
	Tests for the Langevin integrator.
file	langevintestrunners.cpp
	Runner for CPU-based implementation of the Langevin integrator.
file	langevintestrunners.h
	Langevin tests runners.
file	leapfrog.cpp
	Tests for the Leap-Frog integrator.
file	leapfrogtestdata.cpp
	Defines the class to accumulate the data needed for the Leap-Frog integrator tests.
file	leapfrogtestdata.h
	Tests for the Leap-Frog integrator.
file	leapfrogtestrunners.cpp
	Runner for CPU-based implementation of the integrator.
file	leapfrogtestrunners.h
	Leap-Frog tests runners.
file	leapfrogtestrunners_gpu.cpp
	Runner for GPU version of the integrator.
file	settle.cpp
	Tests for SETTLE constraints.
file	settletestdata.cpp
	Defines the class that accumulates SETTLE test data.
file	settletestdata.h
	SETTLE tests header.
file	settletestrunners.cpp
	Defines the test runner for CPU version of SETTLE.
file	settletestrunners.h
	SETTLE tests runners.
file	settletestrunners_gpu.cpp
	Defines the runner for CUDA version of SETTLE.
file	simulationsignal.cpp
	Tests for the mdrun signalling functionality.
file	updategroups.cpp
	Tests for the update groups functionality.
file	wholemoleculetransform.cpp
	Tests for the WholeMoleculeTransform class.
file	update_constrain_gpu.h
	Declaration of high-level functions of GPU implementation of update and constrain class.
file	update_constrain_gpu_impl.cpp
	Implements update and constraints class.
file	update_constrain_gpu_impl.h
	Declares GPU implementation class for update and constraints.
file	update_constrain_gpu_impl_stubs.cpp
	Stub for update and constraints class CPU implementation.
file	update_constrain_gpu_internal.h
	Declares GPU implementations of backend-specific update-constraints functions.
file	update_constrain_gpu_internal_hip.cpp
	Implements backend-specific functions of the update-constraints in HIP.
file	update_constrain_gpu_internal_sycl.cpp
	Implements backend-specific functions of the update-constraints in SYCL.
file	updategroups.h
	Declares the functions for generating update groups.
file	updategroupscog.h
	Declares the UpdateGroupsCog class for managing centers of mass of update groups.
file	vsite.cpp
	Implements the VirtualSitesHandler class and vsite standalone functions.
file	vsite.h
	Declares the VirtualSitesHandler class and vsite standalone functions.
file	wholemoleculetransform.h
	Declares the WholeMolecules class for generating whole molecules.
file	simulation_workload.h
	Declares step, domain-lifetime, and run workload managers.