Neighbor list implementation based on binning particles on a Cartesian grid with cells of the same size as the interaction distance. More...

#include <Cabana_VerletList.hpp>

Collaboration diagram for Cabana::VerletList< MemorySpace, AlgorithmTag, LayoutTag, BuildTag, NumSpaceDim >:

[legend]

Public Types
using	memory_space = MemorySpace
	Kokkos memory space in which the neighbor list data resides.

using	execution_space = typename memory_space::execution_space
	Kokkos default execution space for this memory space.

Public Member Functions
	VerletList ()=default
	Default constructor.

template<class PositionType, template< class, std::size_t, class... > class ArrayType, class... Args>
	VerletList (PositionType x, const std::size_t begin, const std::size_t end, const typename PositionType::value_type neighborhood_radius, const typename PositionType::value_type cell_size_ratio, const ArrayType< typename PositionType::value_type, num_space_dim > grid_min, const ArrayType< typename PositionType::value_type, num_space_dim > grid_max, const std::size_t max_neigh=0, typename std::enable_if<(is_slice< PositionType >::value\|\|Kokkos::is_view< PositionType >::value), int >::type *=0)
	Given a list of particle positions and a neighborhood radius calculate the neighbor list.

template<class PositionType, template< class, std::size_t, class... > class ArrayType, class... Args>
void	build (PositionType x, const std::size_t begin, const std::size_t end, const typename PositionType::value_type neighborhood_radius, const typename PositionType::value_type cell_size_ratio, const ArrayType< typename PositionType::value_type, num_space_dim > grid_min, const ArrayType< typename PositionType::value_type, num_space_dim > grid_max, const std::size_t max_neigh=0, typename std::enable_if<(is_slice< PositionType >::value\|\|Kokkos::is_view< PositionType >::value), int >::type *=0)
	Given a list of particle positions and a neighborhood radius calculate the neighbor list.

template<class PositionType, class RadiusType, template< class, std::size_t, class... > class ArrayType, class... Args>
	VerletList (PositionType x, const std::size_t begin, const std::size_t end, const typename PositionType::value_type background_radius, RadiusType neighborhood_radius, const typename PositionType::value_type cell_size_ratio, const ArrayType< typename PositionType::value_type, num_space_dim > grid_min, const ArrayType< typename PositionType::value_type, num_space_dim > grid_max, const std::size_t max_neigh=0, typename std::enable_if<(is_slice< PositionType >::value\|\|Kokkos::is_view< PositionType >::value), int >::type *=0)
	Given a list of particle positions and a neighborhood radius calculate the neighbor list.

template<class PositionType, template< class, std::size_t, class... > class ArrayType, class... Args>
	VerletList (PositionType x, const typename PositionType::value_type neighborhood_radius, const typename PositionType::value_type cell_size_ratio, const ArrayType< typename PositionType::value_type, num_space_dim > grid_min, const ArrayType< typename PositionType::value_type, num_space_dim > grid_max, const std::size_t max_neigh=0, typename std::enable_if<(is_slice< PositionType >::value\|\|Kokkos::is_view< PositionType >::value), int >::type *=0)
	Given a list of particle positions and a neighborhood radius calculate the neighbor list.

template<class PositionType>
	VerletList (PositionType x, const std::size_t begin, const std::size_t end, const typename PositionType::value_type neighborhood_radius, const typename PositionType::value_type cell_size_ratio, const typename PositionType::value_type grid_min[num_space_dim], const typename PositionType::value_type grid_max[num_space_dim], const std::size_t max_neigh=0, typename std::enable_if<(is_slice< PositionType >::value\|\|Kokkos::is_view< PositionType >::value), int >::type *=0)
	Given a list of particle positions and a neighborhood radius calculate the neighbor list.

template<class PositionType>
	VerletList (PositionType x, const typename PositionType::value_type neighborhood_radius, const typename PositionType::value_type cell_size_ratio, const typename PositionType::value_type grid_min[num_space_dim], const typename PositionType::value_type grid_max[num_space_dim], const std::size_t max_neigh=0, typename std::enable_if<(is_slice< PositionType >::value\|\|Kokkos::is_view< PositionType >::value), int >::type *=0)
	Given a list of particle positions and a neighborhood radius calculate the neighbor list.s.

template<class PositionType, class RadiusType>
	VerletList (PositionType x, const std::size_t begin, const std::size_t end, const typename PositionType::value_type background_radius, RadiusType neighborhood_radius, const typename PositionType::value_type cell_size_ratio, const typename PositionType::value_type grid_min[num_space_dim], const typename PositionType::value_type grid_max[num_space_dim], const std::size_t max_neigh=0, typename std::enable_if<(is_slice< PositionType >::value\|\|Kokkos::is_view< PositionType >::value), int >::type *=0)
	Given a list of particle positions and a neighborhood radius calculate the neighbor list.

template<class PositionType, class RadiusType, template< class, std::size_t, class... > class ArrayType, class... Args>
void	build (PositionType x, const std::size_t begin, const std::size_t end, const typename PositionType::value_type background_radius, RadiusType neighborhood_radius, const typename PositionType::value_type cell_size_ratio, const ArrayType< typename PositionType::value_type, num_space_dim > grid_min, const ArrayType< typename PositionType::value_type, num_space_dim > grid_max, const std::size_t max_neigh=0)
	Given a list of particle positions and a neighborhood radius calculate the neighbor list.

template<class PositionType, template< class, std::size_t, class... > class ArrayType, class... Args>
void	build (PositionType x, const typename PositionType::value_type neighborhood_radius, const typename PositionType::value_type cell_size_ratio, const ArrayType< typename PositionType::value_type, num_space_dim > grid_min, const ArrayType< typename PositionType::value_type, num_space_dim > grid_max, const std::size_t max_neigh=0, typename std::enable_if<(is_slice< PositionType >::value\|\|Kokkos::is_view< PositionType >::value), int >::type *=0)
	VerletList constructor. Given a list of particle positions and a neighborhood radius calculate the neighbor list.

template<class PositionType>
void	build (PositionType x, const std::size_t begin, const std::size_t end, const typename PositionType::value_type neighborhood_radius, const typename PositionType::value_type cell_size_ratio, const typename PositionType::value_type grid_min[num_space_dim], const typename PositionType::value_type grid_max[num_space_dim], const std::size_t max_neigh=0, typename std::enable_if<(is_slice< PositionType >::value\|\|Kokkos::is_view< PositionType >::value), int >::type *=0)
	Given a list of particle positions and a neighborhood radius calculate the neighbor list.

template<class PositionType, class ExecutionSpace>
void	build (ExecutionSpace exec_space, PositionType x, const std::size_t begin, const std::size_t end, const typename PositionType::value_type neighborhood_radius, const typename PositionType::value_type cell_size_ratio, const typename PositionType::value_type grid_min[num_space_dim], const typename PositionType::value_type grid_max[num_space_dim], const std::size_t max_neigh=0, typename std::enable_if<(is_slice< PositionType >::value\|\|Kokkos::is_view< PositionType >::value), int >::type *=0)
	Given a list of particle positions and a neighborhood radius calculate the neighbor list.

template<class PositionType, class RadiusType>
void	build (PositionType x, const std::size_t begin, const std::size_t end, const typename PositionType::value_type background_radius, RadiusType neighborhood_radius, const typename PositionType::value_type cell_size_ratio, const typename PositionType::value_type grid_min[num_space_dim], const typename PositionType::value_type grid_max[num_space_dim], const std::size_t max_neigh=0)
	Given a list of particle positions and a neighborhood radius calculate the neighbor list.

template<class PositionType>
void	build (PositionType x, const typename PositionType::value_type neighborhood_radius, const typename PositionType::value_type cell_size_ratio, const typename PositionType::value_type grid_min[num_space_dim], const typename PositionType::value_type grid_max[num_space_dim], const std::size_t max_neigh=0, typename std::enable_if<(is_slice< PositionType >::value\|\|Kokkos::is_view< PositionType >::value), int >::type *=0)
	Given a list of particle positions and a neighborhood radius calculate the neighbor list.

template<class PositionType, class RadiusType, class ExecutionSpace>
void	build (ExecutionSpace exec_space, PositionType x, const std::size_t begin, const std::size_t end, const typename PositionType::value_type background_radius, RadiusType neighborhood_radius, const typename PositionType::value_type cell_size_ratio, const typename PositionType::value_type grid_min[num_space_dim], const typename PositionType::value_type grid_max[num_space_dim], const std::size_t max_neigh=0)
	Given a list of particle positions and a neighborhood radius calculate the neighbor list.

template<class PositionType, class ExecutionSpace, template< class, std::size_t, class... > class ArrayType, class... Args>
void	build (ExecutionSpace, PositionType x, const std::size_t begin, const std::size_t end, const typename PositionType::value_type neighborhood_radius, const typename PositionType::value_type cell_size_ratio, const ArrayType< typename PositionType::value_type, num_space_dim > grid_min, const ArrayType< typename PositionType::value_type, num_space_dim > grid_max, const std::size_t max_neigh=0, typename std::enable_if<(is_slice< PositionType >::value\|\|Kokkos::is_view< PositionType >::value), int >::type *=0)
	Given a list of particle positions and a neighborhood radius calculate the neighbor list.

template<class PositionType, class RadiusType, class ExecutionSpace, template< class, std::size_t, class... > class ArrayType, class... Args>
void	build (ExecutionSpace, PositionType x, const std::size_t begin, const std::size_t end, const typename PositionType::value_type background_radius, RadiusType neighborhood_radius, const typename PositionType::value_type cell_size_ratio, const ArrayType< typename PositionType::value_type, num_space_dim > grid_min, const ArrayType< typename PositionType::value_type, num_space_dim > grid_max, const std::size_t max_neigh=0)
	Given a list of particle positions and a neighborhood radius calculate the neighbor list.

KOKKOS_INLINE_FUNCTION void	setNeighbor (const std::size_t particle_index, const std::size_t neighbor_index, const int new_index) const
	Modify a neighbor in the list; for example, mark it as a broken bond.

Public Attributes
VerletListData< memory_space, LayoutTag >	_data
	Verlet list data.

Static Public Attributes
static constexpr std::size_t	num_space_dim = NumSpaceDim
	Spatial dimension.

Detailed Description

template<class MemorySpace, class AlgorithmTag, class LayoutTag, class BuildTag = TeamVectorOpTag, std::size_t NumSpaceDim = 3>
class Cabana::VerletList< MemorySpace, AlgorithmTag, LayoutTag, BuildTag, NumSpaceDim >

Neighbor list implementation based on binning particles on a Cartesian grid with cells of the same size as the interaction distance.

Template Parameters

MemorySpace	The Kokkos memory space for storing the neighbor list.
AlgorithmTag	Tag indicating whether to build a full or half neighbor list.
LayoutTag	Tag indicating whether to use a CSR or 2D data layout.
BuildTag	Tag indicating whether to use hierarchical team or team vector parallelism when building neighbor lists.

Neighbor list implementation most appropriate for somewhat regularly distributed particles due to the use of a Cartesian grid.

Constructor & Destructor Documentation

◆ VerletList() [1/3]

template<class MemorySpace, class AlgorithmTag, class LayoutTag, class BuildTag = TeamVectorOpTag, std::size_t NumSpaceDim = 3>

template<class PositionType, template< class, std::size_t, class... > class ArrayType, class... Args>

Cabana::VerletList< MemorySpace, AlgorithmTag, LayoutTag, BuildTag, NumSpaceDim >::VerletList	(	PositionType	x,
		const std::size_t	begin,
		const std::size_t	end,
		const typename PositionType::value_type	neighborhood_radius,
		const typename PositionType::value_type	cell_size_ratio,
		const ArrayType< typename PositionType::value_type, num_space_dim >	grid_min,
		const ArrayType< typename PositionType::value_type, num_space_dim >	grid_max,
		const std::size_t	max_neigh = 0,
		typename std::enable_if<(is_slice< PositionType >::value\|\|Kokkos::is_view< PositionType >::value), int >::type *	= 0 )

inline

Given a list of particle positions and a neighborhood radius calculate the neighbor list.

Parameters

x	The particle positions
begin	The beginning particle index to compute neighbors for.
end	The end particle index to compute neighbors for.
neighborhood_radius	The radius of the neighborhood. Particles within this radius are considered neighbors. This is effectively the grid cell size in each dimension.
cell_size_ratio	The ratio of the cell size in the Cartesian grid to the neighborhood radius. For example, if the cell size ratio is 0.5 then the cells will be half the size of the neighborhood radius in each dimension.
grid_min	The minimum value of the grid containing the particles in each dimension.
grid_max	The maximum value of the grid containing the particles in each dimension.
max_neigh	Optional maximum number of neighbors per particle to pre-allocate the neighbor list. Potentially avoids recounting with 2D layout only.

Particles outside of the neighborhood radius will not be considered neighbors. Only compute the neighbors of those that are within the given range. All particles are candidates for being a neighbor, regardless of whether or not they are in the range.

◆ VerletList() [2/3]

template<class MemorySpace, class AlgorithmTag, class LayoutTag, class BuildTag = TeamVectorOpTag, std::size_t NumSpaceDim = 3>

template<class PositionType, class RadiusType, template< class, std::size_t, class... > class ArrayType, class... Args>

Cabana::VerletList< MemorySpace, AlgorithmTag, LayoutTag, BuildTag, NumSpaceDim >::VerletList	(	PositionType	x,
		const std::size_t	begin,
		const std::size_t	end,
		const typename PositionType::value_type	background_radius,
		RadiusType	neighborhood_radius,
		const typename PositionType::value_type	cell_size_ratio,
		const ArrayType< typename PositionType::value_type, num_space_dim >	grid_min,
		const ArrayType< typename PositionType::value_type, num_space_dim >	grid_max,
		const std::size_t	max_neigh = 0,
		typename std::enable_if<(is_slice< PositionType >::value\|\|Kokkos::is_view< PositionType >::value), int >::type *	= 0 )

inline

Given a list of particle positions and a neighborhood radius calculate the neighbor list.

Parameters

x	The slice containing the particle positions
begin	The beginning particle index to compute neighbors for.
end	The end particle index to compute neighbors for.
background_radius	The radius of the neighborhood used for the background grid cells in each dimension.
neighborhood_radius	The radius of the neighborhood per particle. Particles within this radius are considered neighbors.
cell_size_ratio	The ratio of the cell size in the Cartesian grid to the neighborhood radius. For example, if the cell size ratio is 0.5 then the cells will be half the size of the neighborhood radius in each dimension.
grid_min	The minimum value of the grid containing the particles in each dimension.
grid_max	The maximum value of the grid containing the particles in each dimension.
max_neigh	Optional maximum number of neighbors per particle to pre-allocate the neighbor list. Potentially avoids recounting with 2D layout only.

Particles outside of the neighborhood radius will not be considered neighbors. Only compute the neighbors of those that are within the given range. All particles are candidates for being a neighbor, regardless of whether or not they are in the range.

◆ VerletList() [3/3]

template<class MemorySpace, class AlgorithmTag, class LayoutTag, class BuildTag = TeamVectorOpTag, std::size_t NumSpaceDim = 3>

template<class PositionType, template< class, std::size_t, class... > class ArrayType, class... Args>

Cabana::VerletList< MemorySpace, AlgorithmTag, LayoutTag, BuildTag, NumSpaceDim >::VerletList	(	PositionType	x,
		const typename PositionType::value_type	neighborhood_radius,
		const typename PositionType::value_type	cell_size_ratio,
		const ArrayType< typename PositionType::value_type, num_space_dim >	grid_min,
		const ArrayType< typename PositionType::value_type, num_space_dim >	grid_max,
		const std::size_t	max_neigh = 0,
		typename std::enable_if<(is_slice< PositionType >::value\|\|Kokkos::is_view< PositionType >::value), int >::type *	= 0 )

inline

Given a list of particle positions and a neighborhood radius calculate the neighbor list.

Parameters

x	The slice containing the particle positions
neighborhood_radius	The radius of the neighborhood. Particles within this radius are considered neighbors. This is effectively the grid cell size in each dimension.
cell_size_ratio	The ratio of the cell size in the Cartesian grid to the neighborhood radius. For example, if the cell size ratio is 0.5 then the cells will be half the size of the neighborhood radius in each dimension.
grid_min	The minimum value of the grid containing the particles in each dimension.
grid_max	The maximum value of the grid containing the particles in each dimension.
max_neigh	Optional maximum number of neighbors per particle to pre-allocate the neighbor list. Potentially avoids recounting with 2D layout only.

Member Function Documentation

◆ build() [1/3]

template<class MemorySpace, class AlgorithmTag, class LayoutTag, class BuildTag = TeamVectorOpTag, std::size_t NumSpaceDim = 3>

template<class PositionType, class RadiusType, template< class, std::size_t, class... > class ArrayType, class... Args>

void Cabana::VerletList< MemorySpace, AlgorithmTag, LayoutTag, BuildTag, NumSpaceDim >::build	(	PositionType	x,
		const std::size_t	begin,
		const std::size_t	end,
		const typename PositionType::value_type	background_radius,
		RadiusType	neighborhood_radius,
		const typename PositionType::value_type	cell_size_ratio,
		const ArrayType< typename PositionType::value_type, num_space_dim >	grid_min,
		const ArrayType< typename PositionType::value_type, num_space_dim >	grid_max,
		const std::size_t	max_neigh = 0 )

inline

Given a list of particle positions and a neighborhood radius calculate the neighbor list.

Parameters

x	The particle positions
begin	The beginning particle index to compute neighbors for.
end	The end particle index to compute neighbors for.
background_radius	The radius of the neighborhood used for the background grid cells in each dimension.
neighborhood_radius	The radius of the neighborhood per particle. Particles within this radius are considered neighbors.
cell_size_ratio	The ratio of the cell size in the Cartesian grid to the neighborhood radius. For example, if the cell size ratio is 0.5 then the cells will be half the size of the neighborhood radius in each dimension.
grid_min	The minimum value of the grid containing the particles in each dimension.
grid_max	The maximum value of the grid containing the particles in each dimension.
max_neigh	Optional maximum number of neighbors per particle to pre-allocate the neighbor list. Potentially avoids recounting with 2D layout only.

Particles outside of the neighborhood radius will not be considered neighbors. Only compute the neighbors of those that are within the given range. All particles are candidates for being a neighbor, regardless of whether or not they are in the range.

◆ build() [2/3]

template<class MemorySpace, class AlgorithmTag, class LayoutTag, class BuildTag = TeamVectorOpTag, std::size_t NumSpaceDim = 3>

template<class PositionType, template< class, std::size_t, class... > class ArrayType, class... Args>

void Cabana::VerletList< MemorySpace, AlgorithmTag, LayoutTag, BuildTag, NumSpaceDim >::build	(	PositionType	x,
		const std::size_t	begin,
		const std::size_t	end,
		const typename PositionType::value_type	neighborhood_radius,
		const typename PositionType::value_type	cell_size_ratio,
		const ArrayType< typename PositionType::value_type, num_space_dim >	grid_min,
		const ArrayType< typename PositionType::value_type, num_space_dim >	grid_max,
		const std::size_t	max_neigh = 0,
		typename std::enable_if<(is_slice< PositionType >::value\|\|Kokkos::is_view< PositionType >::value), int >::type *	= 0 )

inline

Given a list of particle positions and a neighborhood radius calculate the neighbor list.

Parameters

x	The particle positions
begin	The beginning particle index to compute neighbors for.
end	The end particle index to compute neighbors for.
neighborhood_radius	The radius of the neighborhood. Particles within this radius are considered neighbors. This is effectively the grid cell size in each dimension.
cell_size_ratio	The ratio of the cell size in the Cartesian grid to the neighborhood radius. For example, if the cell size ratio is 0.5 then the cells will be half the size of the neighborhood radius in each dimension.
grid_min	The minimum value of the grid containing the particles in each dimension.
grid_max	The maximum value of the grid containing the particles in each dimension.
max_neigh	Optional maximum number of neighbors per particle to pre-allocate the neighbor list. Potentially avoids recounting with 2D layout only.

Particles outside of the neighborhood radius will not be considered neighbors. Only compute the neighbors of those that are within the given range. All particles are candidates for being a neighbor, regardless of whether or not they are in the range.

◆ build() [3/3]

template<class MemorySpace, class AlgorithmTag, class LayoutTag, class BuildTag = TeamVectorOpTag, std::size_t NumSpaceDim = 3>

template<class PositionType, template< class, std::size_t, class... > class ArrayType, class... Args>

void Cabana::VerletList< MemorySpace, AlgorithmTag, LayoutTag, BuildTag, NumSpaceDim >::build	(	PositionType	x,
		const typename PositionType::value_type	neighborhood_radius,
		const typename PositionType::value_type	cell_size_ratio,
		const ArrayType< typename PositionType::value_type, num_space_dim >	grid_min,
		const ArrayType< typename PositionType::value_type, num_space_dim >	grid_max,
		const std::size_t	max_neigh = 0,
		typename std::enable_if<(is_slice< PositionType >::value\|\|Kokkos::is_view< PositionType >::value), int >::type *	= 0 )

inline

VerletList constructor. Given a list of particle positions and a neighborhood radius calculate the neighbor list.

Parameters

x	The particle positions
neighborhood_radius	The radius of the neighborhood. Particles within this radius are considered neighbors. This is effectively the grid cell size in each dimension.
cell_size_ratio	The ratio of the cell size in the Cartesian grid to the neighborhood radius. For example, if the cell size ratio is 0.5 then the cells will be half the size of the neighborhood radius in each dimension.
grid_min	The minimum value of the grid containing the particles in each dimension.
grid_max	The maximum value of the grid containing the particles in each dimension.
max_neigh	Optional maximum number of neighbors per particle to pre-allocate the neighbor list. Potentially avoids recounting with 2D layout only.

The documentation for this class was generated from the following file:

core/src/Cabana_VerletList.hpp

Public Types

Public Member Functions

Public Attributes

Static Public Attributes

Detailed Description

Constructor & Destructor Documentation

◆ VerletList() [1/3]

◆ VerletList() [2/3]

◆ VerletList() [3/3]

Member Function Documentation

◆ build() [1/3]

◆ build() [2/3]

◆ build() [3/3]