Non-bonded pair interactions

Collaboration diagram for Non-bonded pair interactions:

Description

Implements non-bonded pair interaction functionality for NxM atom clusters.

This module provides methods to, very efficiently, compute non-bonded pair interactions on CPUs as well as accelerators. It also provides a method to construct the NxM atom-cluster pair-list required for computing these non-bonded iteractions.

Files
file	atomdata.h
	Functionality for per-atom data in the nbnxm module.
file	bench_coords.h
	This file defines a box with 1000 SPC/E water molecules for use in benchmarks.
file	bench_setup.cpp
	This file defines functions for setting up kernel benchmarks.
file	bench_setup.h
	This file declares functions for setting up kernel benchmarks.
file	bench_system.cpp
	This file defines functions for setting up a benchmark system.
file	bench_system.h
	This file declares functions for setting up a benchmark system.
file	boundingbox.h
	Declares and defines the BoundingBox class.
file	boundingbox_simd.h
	Declares sizes and boolean macros for bouding boxes handled with SIMD code.
file	boundingboxdistance.h
	Declares and defines functions for computing distances between bounding boxes.
file	clusterdistancekerneltype.h
	Declares the ClusterDistanceKernelType enum.
file	nbnxm_cuda.h
	Declares nbnxn cuda cache and texture helper functions.
file	nbnxm_cuda_types.h
	Data types used internally in the nbnxn_cuda module.
file	exclusionchecker.cpp
	This file defines functions to reduce and check exclusion counts.
file	exclusionchecker.h
	This file declares functionality for checking whether all exclusions are present in the pairlist.
file	freeenergydispatch.h
	Declares the free-energy kernel dispatch class.
file	freeenergykernel.h
	Declares and defines the AtomPairlist class.
file	gpu_common.h
	Common functions for the different NBNXN GPU implementations.
file	gpu_common_utils.h
	Implements common util routines for different NBNXN GPU implementations.
file	gpu_data_mgmt.h
	Declare interface for GPU data transfer for NBNXN module.
file	gpu_jit_support.h
	Declares functions that support JIT compilation (e.g. for OpenCL)
file	gpu_types_common.h
	Implements common internal types for different NBNXN GPU implementations.
file	grid.cpp
	Implements the Grid class.
file	grid.h
	Declares the Grid class.
file	gridset.cpp
	Implements the GridSet class.
file	gridset.h
	Declares the GridSet class.
file	gridsetdata.h
	Declares the GridSetData struct which holds grid data that is shared over all grids.
file	nbnxm_hip.cpp
	Data management and kernel launch functions for nbnxm hip.
file	nbnxm_hip_kernel.cpp
	NBNXM HIP kernels.
file	nbnxm_hip_kernel.h
	Declares nbnxn hip helper functions.
file	nbnxm_hip_kernel_body.h
	NBNXM HIP kernels.
file	nbnxm_hip_kernel_body_f_noprune.cpp
	Explicitly instantiate NBNXM HIP kernels, F-only, no pruning.
file	nbnxm_hip_kernel_body_f_prune.cpp
	Explicitly instantiate NBNXM HIP kernels, F-only, with pruning.
file	nbnxm_hip_kernel_body_fv_noprune.cpp
	Explicitly instantiate NBNXM HIP kernels, F+V, no pruning.
file	nbnxm_hip_kernel_body_fv_prune.cpp
	Explicitly instantiate NBNXM HIP kernels, F+V, with pruning.
file	nbnxm_hip_kernel_pruneonly.cpp
	NBNXM HIP prune only kernels.
file	nbnxm_hip_kernel_pruneonly.h
	Declares nbnxn hip helper functions.
file	nbnxm_hip_kernel_sci_sort.cpp
	Explicitly instantiate NBNXM HIP kernel for sci sorting.
file	nbnxm_hip_kernel_sci_sort.h
	HIP bucket sci sort kernel.
file	nbnxm_hip_kernel_utils.h
	Utility constant and function declaration for the HIP non-bonded kernels. This header should be included once at the top level, just before the kernels are included (has to be preceded by nbnxn_hip_types.h).
file	nbnxm_hip_types.h
	Data types used internally in the nbnxn_hip module.
file	kernel_common.cpp
	Implements utility functions used by all nbnxm CPU kernels.
file	kernel_common.h
	Declares the nbnxm pair interaction kernel function types and kind counts, also declares utility functions used in nbnxm_kernel.cpp.
file	kernel_gpu_ref.h
	Declares GPU reference kernel.
file	kernel_ref_1x1.h
	Declares CPU reference kernels.
file	kernel_ref_4x4.h
	Declares CPU reference kernels.
file	kernel_ref_prune.h
	Declares the C reference pruning only kernel.
file	nbnxm.cpp
	Implements the Nbnxm class.
file	nbnxm.h
	This file contains the public interface of the nbnxm module that implements the NxM atom cluster non-bonded algorithm to efficiently compute pair forces.
file	nbnxm_enums.h
	Nbnxm internal enumerations.
file	nbnxm_geometry.h
	Declares the geometry-related functionality.
file	nbnxm_gpu.h
	Declare interface for GPU execution for NBNXN module.
file	nbnxm_gpu_buffer_ops.cpp
	Common code for GPU buffer operations, namely the coordinate layout conversion.
file	nbnxm_gpu_buffer_ops_internal.h
	Wrapper for the backend-specific coordinate layout conversion functionality.
file	nbnxm_gpu_data_mgmt.cpp
	Define common implementation of nbnxm_gpu_data_mgmt.h.
file	nbnxm_gpu_data_mgmt.h
	Declare common functions for NBNXM GPU data management.
file	nbnxm_setup.cpp
	Common functions for the different NBNXN GPU implementations.
file	nbnxm_simd.h
	Defines constants used to know which nbNxM kernel flavours (4xM or 2xMM) can be supported by the SIMD layer in use.
file	nbnxm_gpu_buffer_ops_internal_ocl.cpp
	Define OpenCL implementation for transforming position coordinates from rvec to nbnxm layout.
file	nbnxm_ocl.cpp
	Define OpenCL implementation of nbnxm_gpu.h.
file	nbnxm_ocl_consts.h
	Declares constants for OpenCL code.
file	nbnxm_ocl_data_mgmt.cpp
	Define OpenCL implementation of nbnxm_gpu_data_mgmt.h.
file	nbnxm_ocl_jit_support.cpp
	Defines functions that support JIT compilation (e.g. for OpenCL)
file	nbnxm_ocl_types.h
	Data types used internally in the nbnxm_ocl module.
file	pairlist_imask.h
	Declares and defines pairlist interaction mask generation functions.
file	pairlist_simd_kernel.cpp
	Defines the SIMD cluster pair distance kernel and helpers.
file	pairlist_simd_kernel.h
	Declares the SIMD cluster pair distance kernel and helpers.
file	pairlist_tuning.cpp
	Implements functions for tuning adjustable parameters for the nbnxn non-bonded search and interaction kernels.
file	pairlist_tuning.h
	Declares functions for tuning adjustable parameters for the nbnxn non-bonded search and interaction kernels.
file	pairlistparams.cpp
	Implements the PairlistParams constructor.
file	pairlistparams.h
	Declares the PairlistType enum and PairlistParams class.
file	pairlistset.cpp
	Implements functionality for PairlistSet.
file	pairlistset.h
	Declares the PairlistSet class.
file	pairlistsets.cpp
	Implements functionality for PairlistSets.
file	pairlistsets.h
	Declares the PairlistSets class.
file	pairlistwork.cpp
	Implements constructors for NbnxnPairlistGpuWork.
file	pairlistwork.h
	Declares working data structures for the CPU and GPU pairlists.
file	pairsearch.cpp
	Implements the PairSearch class.
file	pairsearch.h
	Declares the PairSearch class and helper structs.
file	simd_kernel.h
	Declares and defines the NBNxM SIMD pair interaction kernel function.
file	simd_load_store_functions.h
	Defines functions to load data to and store data from SIMD registers for the SIMD 4xM and 2xMM kernels.
file	simd_prune_kernel.h
	Declares the NBNxM SIMD pruning only kernel.
file	nbnxm_gpu_buffer_ops_internal_sycl.cpp
	SYCL implementation of coordinate layout conversion kernel and its wrapper.
file	nbnxm_sycl.cpp
	Data management and kernel launch functions for nbnxm sycl.
file	nbnxm_sycl_data_mgmt.cpp
	Stubs of functions that must be defined by nbnxm sycl implementation.
file	nbnxm_sycl_kernel.cpp
	NBNXM SYCL kernels.
file	nbnxm_sycl_kernel.h
	Declares nbnxn sycl helper functions.
file	nbnxm_sycl_kernel_body.h
	NBNXM SYCL kernels.
file	nbnxm_sycl_kernel_body_f_noprune.cpp
	Explicitly instantiate NBNXM SYCL kernels, F-only, no pruning.
file	nbnxm_sycl_kernel_body_f_prune.cpp
	Explicitly instantiate NBNXM SYCL kernels, F-only, with pruning.
file	nbnxm_sycl_kernel_body_fv_noprune.cpp
	Explicitly instantiate NBNXM SYCL kernels, F+V, no pruning.
file	nbnxm_sycl_kernel_body_fv_prune.cpp
	Explicitly instantiate NBNXM SYCL kernels, F+V, with pruning.
file	nbnxm_sycl_kernel_pruneonly.cpp
	NBNXM SYCL kernels.
file	nbnxm_sycl_kernel_pruneonly.h
	Declares nbnxn sycl helper functions.
file	nbnxm_sycl_kernel_utils.h
	Helper functions and constants for SYCL NBNXM kernels.
file	nbnxm_sycl_types.h
	Data types used internally in the nbnxm_sycl module.
file	exclusions.cpp
	Tests for exclusions in the Nbnxm CPU pairlists.
file	kernel_test.cpp
	Tests for NBNxM pair kernel forces and energies.
file	kernelsetup.cpp
	Tests for Setup of kernels.
file	pairlist.cpp
	Tests for gpu pairlist datastructure memory handling.
file	plainpairlist.cpp
	Tests for the plain pairlist extraction functionality.
file	simd_energy_accumulator.cpp
	Tests for the EnergyAccumulator class.
file	spc81_coords.h
	This file defines a box with 81 SPC/E water molecules, 243 atoms, for use in tests.
file	testsystem.cpp
	Implements the TestSystem class.
file	testsystem.h
	Declares the TestSystem class used for testing NBNxM functionality.