vesin.cpp File Reference

#include "vesin.h"
#include <cassert>
#include <cstdlib>
#include <cstring>
#include <algorithm>
#include <numeric>
#include <tuple>
#include <vector>
#include <array>
#include <string>
#include <cmath>
#include <stdexcept>
#include <iostream>

Classes
class	PLMD::metatomic::vesin::BoundingBox
struct	PLMD::metatomic::vesin::cpu::CellList::Cell
class	PLMD::metatomic::vesin::cpu::CellList
	The cell list is used to sort atoms inside bins/cells. More...
struct	PLMD::metatomic::vesin::cuda::CellListBuffers
	Buffers for cell list-based neighbor search. More...
struct	PLMD::metatomic::vesin::CellShift
	A cell shift represents the displacement along cell axis between the actual position of an atom and a periodic image of this atom. More...
struct	PLMD::metatomic::vesin::cuda::CudaNeighborListExtras
class	PLMD::metatomic::vesin::cpu::GrowableNeighborList
	Wrapper around VesinNeighborList that behaves like a std::vector, automatically growing memory allocations. More...
struct	PLMD::metatomic::vesin::Matrix
struct	PLMD::metatomic::vesin::cpu::CellList::Point
	the cells themselves are a list of points & corresponding shift to place the point inside the cell More...
struct	PLMD::metatomic::vesin::Vector

Namespaces
namespace	PLMD
namespace	PLMD::metatomic
namespace	PLMD::metatomic::vesin
namespace	PLMD::metatomic::vesin::cpu
namespace	PLMD::metatomic::vesin::cuda

Macros
#define	MAX_NUMBER_OF_CELLS   1e5
	Maximal number of cells, we need to use this to prevent having too many cells with a small bounding box and a large cutoff.
#define	VESIN_CPU_CELL_LIST_HPP
#define	VESIN_CUDA_AT_LEAST_PAIRS_PER_POINT   128
	Default value for the number of pairs per points in the CUDA implementation.
#define	VESIN_CUDA_HPP
#define	VESIN_MATH_HPP
#define	VESIN_TYPES_HPP

Typedefs
template<typename scalar_t, size_t N>
using	array_ptr = scalar_t (*)[N]

Functions
template<typename scalar_t, size_t N>
static array_ptr< scalar_t, N >	alloc (array_ptr< scalar_t, N > ptr, size_t size, size_t new_size)
template<typename scalar_t>
static scalar_t *	alloc (scalar_t *ptr, size_t size, size_t new_size)
static std::tuple< int32_t, int32_t >	divmod (int32_t a, size_t b)
	Function to compute both quotient and remainder of the division of a by b.
static std::tuple< std::array< int32_t, 3 >, std::array< int32_t, 3 > >	divmod (std::array< int32_t, 3 > a, std::array< size_t, 3 > b)
	Apply the divmod function to three components at the time.
void	PLMD::metatomic::vesin::cpu::free_neighbors (VesinNeighborList &neighbors)
void	PLMD::metatomic::vesin::cuda::free_neighbors (VesinNeighborList &neighbors)
	Frees GPU memory associated with a VesinNeighborList.
CudaNeighborListExtras *	PLMD::metatomic::vesin::cuda::get_cuda_extras (VesinNeighborList *neighbors)
	Get the CudaNeighborListExtras stored inside VesinNeighborList's opaque pointer.
void	PLMD::metatomic::vesin::cpu::neighbors (const Vector *points, size_t n_points, BoundingBox box, VesinOptions options, VesinNeighborList &neighbors)
void	PLMD::metatomic::vesin::cuda::neighbors (const double(*points)[3], size_t n_points, const double box[3][3], const bool periodic[3], VesinOptions options, VesinNeighborList &neighbors)
	Computes the neighbor list on the GPU.
Vector	PLMD::metatomic::vesin::operator* (double scalar, Vector vector)
Vector	PLMD::metatomic::vesin::operator* (Matrix matrix, Vector vector)
Vector	PLMD::metatomic::vesin::operator* (Vector vector, double scalar)
Vector	PLMD::metatomic::vesin::operator* (Vector vector, Matrix matrix)
CellShift	PLMD::metatomic::vesin::operator+ (CellShift a, CellShift b)
Vector	PLMD::metatomic::vesin::operator+ (Vector u, Vector v)
CellShift	PLMD::metatomic::vesin::operator- (CellShift a, CellShift b)
Vector	PLMD::metatomic::vesin::operator- (Vector u, Vector v)
void	vesin_free (VesinNeighborList *neighbors)
int	vesin_neighbors (const double(*points)[3], size_t n_points, const double box[3][3], const bool periodic[3], VesinDevice device, VesinOptions options, VesinNeighborList *neighbors, const char **error_message)

Variables
thread_local std::string	LAST_ERROR

Macro Definition Documentation

MAX_NUMBER_OF_CELLS

#define MAX_NUMBER_OF_CELLS   1e5

Maximal number of cells, we need to use this to prevent having too many cells with a small bounding box and a large cutoff.

VESIN_CPU_CELL_LIST_HPP

#define VESIN_CPU_CELL_LIST_HPP

VESIN_CUDA_AT_LEAST_PAIRS_PER_POINT

#define VESIN_CUDA_AT_LEAST_PAIRS_PER_POINT   128

Default value for the number of pairs per points in the CUDA implementation.

Unless VESIN_CUDA_MAX_PAIRS_PER_POINT is set in the environement, the maximal number of pairs is n_points * / max(VESIN_CUDA_AT_LEAST_PAIRS_PER_POINT, cutoff^3). This can be overriden at compile time.

VESIN_CUDA_HPP

#define VESIN_CUDA_HPP

VESIN_MATH_HPP

#define VESIN_MATH_HPP

VESIN_TYPES_HPP

#define VESIN_TYPES_HPP

Typedef Documentation

array_ptr

template<typename scalar_t, size_t N>

using array_ptr = scalar_t (*)[N]

Function Documentation

alloc() [1/2]

template<typename scalar_t, size_t N>

static array_ptr< scalar_t, N > alloc ( array_ptr< scalar_t, N > ptr, size_t size, size_t new_size )

static

alloc() [2/2]

template<typename scalar_t>

static scalar_t * alloc ( scalar_t * ptr, size_t size, size_t new_size )

static

divmod() [1/2]

static std::tuple< int32_t, int32_t > divmod ( int32_t a, size_t b )

static

Function to compute both quotient and remainder of the division of a by b.

This function follows Python convention, making sure the remainder have the same sign as b.

divmod() [2/2]

static std::tuple< std::array< int32_t, 3 >, std::array< int32_t, 3 > > divmod ( std::array< int32_t, 3 > a, std::array< size_t, 3 > b )

static

Apply the divmod function to three components at the time.

vesin_free()

void vesin_free

(

VesinNeighborList *

neighbors

)

vesin_neighbors()

int vesin_neighbors	(	const double(*)	points[3],
		size_t	n_points,
		const double	box[3][3],
		const bool	periodic[3],
		VesinDevice	device,
		VesinOptions	options,
		VesinNeighborList *	neighbors,
		const char **	error_message )

Variable Documentation

LAST_ERROR

thread_local std::string LAST_ERROR