vesin.cpp File Reference

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

Classes
class	PLMD::metatensor::vesin::BoundingBox
struct	PLMD::metatensor::vesin::cpu::CellList::Cell
class	PLMD::metatensor::vesin::cpu::CellList
	The cell list is used to sort atoms inside bins/cells. More...
struct	PLMD::metatensor::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...
class	PLMD::metatensor::vesin::cpu::GrowableNeighborList
	Wrapper around VesinNeighborList that behaves like a std::vector, automatically growing memory allocations. More...
struct	PLMD::metatensor::vesin::Matrix
struct	PLMD::metatensor::vesin::cpu::CellList::Point
	the cells themselves are a list of points & corresponding shift to place the point inside the cell More...
struct	PLMD::metatensor::vesin::Vector

Namespaces
	PLMD
	PLMD::metatensor
	PLMD::metatensor::vesin
	PLMD::metatensor::vesin::cpu

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. More...
#define	VESIN_CPU_CELL_LIST_HPP
#define	VESIN_MATH_HPP
#define	VESIN_TYPES_HPP

Functions
template<typename scalar_t >
static scalar_t *	alloc (scalar_t *ptr, size_t size, size_t new_size)
template<typename scalar_t , size_t N>
static scalar_t(*	alloc (scalar_t(*ptr)[N], size_t size, size_t new_size))[N]
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. More...
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. More...
void	PLMD::metatensor::vesin::cpu::free_neighbors (VesinNeighborList &neighbors)
void	PLMD::metatensor::vesin::cpu::neighbors (const Vector *points, size_t n_points, BoundingBox cell, VesinOptions options, VesinNeighborList &neighbors)
Vector	PLMD::metatensor::vesin::operator* (double scalar, Vector vector)
Vector	PLMD::metatensor::vesin::operator* (Matrix matrix, Vector vector)
Vector	PLMD::metatensor::vesin::operator* (Vector vector, double scalar)
Vector	PLMD::metatensor::vesin::operator* (Vector vector, Matrix matrix)
CellShift	PLMD::metatensor::vesin::operator+ (CellShift a, CellShift b)
Vector	PLMD::metatensor::vesin::operator+ (Vector u, Vector v)
CellShift	PLMD::metatensor::vesin::operator- (CellShift a, CellShift b)
Vector	PLMD::metatensor::vesin::operator- (Vector u, Vector v)
void	vesin_free (VesinNeighborList *neighbors)
	Free all allocated memory inside a VesinNeighborList, according the it's device. More...
int	vesin_neighbors (const double(*points)[3], size_t n_points, const double box[3][3], bool periodic, VesinDevice device, VesinOptions options, VesinNeighborList *neighbors, const char **error_message)
	Compute a neighbor list. More...

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_MATH_HPP

#define VESIN_MATH_HPP

VESIN_TYPES_HPP

#define VESIN_TYPES_HPP

Function Documentation

alloc() [1/2]

template<typename scalar_t >

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

static

alloc() [2/2]

template<typename scalar_t , size_t N>

static scalar_t(* alloc ( scalar_t(*)  ptr[N], size_t  size, size_t  new_size  ) )[N]

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

)

Free all allocated memory inside a VesinNeighborList, according the it's device.

vesin_neighbors()

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

Compute a neighbor list.

The data is returned in a VesinNeighborList. For an initial call, the VesinNeighborList should be zero-initialized (or default-initalized in C++). The VesinNeighborList can be re-used across calls to this functions to re-use memory allocations, and once it is no longer needed, users should call vesin_free to release the corresponding memory.

Parameters

points	positions of all points in the system;
n_points	number of elements in the points array
box	bounding box for the system. If the system is non-periodic, this is ignored. This should contain the three vectors of the bounding box, one vector per row of the matrix.
periodic	is the system using periodic boundary conditions?
device	device where the points and box data is allocated.
options	options for the calculation
neighbors	non-NULL pointer to VesinNeighborList that will be used to store the computed list of neighbors.
error_message	Pointer to a char* that wil be set to the error message if this function fails. This does not need to be freed when no longer needed.

Variable Documentation

LAST_ERROR

thread_local std::string LAST_ERROR