Functions to maintain link cell structures for fast pair finding. More...

#include "linkCells.h"
#include <stdio.h>
#include <string.h>
#include <assert.h>
#include <math.h>
#include "parallel.h"
#include "memUtils.h"
#include "decomposition.h"
#include "performanceTimers.h"
#include "CoMDTypes.h"

Include dependency graph for linkCells.c:

Go to the source code of this file.

Macros
#define	MIN(A, B) ((A) < (B) ? (A) : (B))

#define	MAX(A, B) ((A) > (B) ? (A) : (B))

Functions
static void	copyAtom (LinkCell boxes, Atoms atoms, int iAtom, int iBox, int jAtom, int jBox)
	Copy atom iAtom in link cell iBox to atom jAtom in link cell jBox. More...

static int	getBoxFromCoord (LinkCell *boxes, real_t rr[3])
	Get the index of the link cell that contains the specified coordinate. More...

static void	emptyHaloCells (LinkCell *boxes)
	Set the number of atoms to zero in all halo link cells. More...

static void	getTuple (LinkCell boxes, int iBox, int ixp, int iyp, int izp)
	Get the grid coordinates of the link cell with index iBox. More...

LinkCell *	initLinkCells (const Domain *domain, real_t cutoff)
	In CoMD 1.1, atoms are stored in link cells. More...

void	destroyLinkCells (LinkCell **boxes)

int	getNeighborBoxes (LinkCell boxes, int iBox, int nbrBoxes)

void	putAtomInBox (LinkCell boxes, Atoms atoms, const int gid, const int iType, const real_t x, const real_t y, const real_t z, const real_t px, const real_t py, const real_t pz)

int	getBoxFromTuple (LinkCell *boxes, int ix, int iy, int iz)
	Calculates the link cell index from the grid coords. More...

void	moveAtom (LinkCell boxes, Atoms atoms, int iId, int iBox, int jBox)
	Move an atom from one link cell to another. More...

void	updateLinkCells (LinkCell boxes, Atoms atoms)
	Update link cell data structures when the atoms have moved. More...

int	maxOccupancy (LinkCell *boxes)

Detailed Description

Functions to maintain link cell structures for fast pair finding.

Definition in file linkCells.c.

Macro Definition Documentation

#define MAX	(	A,
		B
	)	((A) > (B) ? (A) : (B))

Definition at line 18 of file linkCells.c.

#define MIN	(	A,
		B
	)	((A) < (B) ? (A) : (B))

Definition at line 17 of file linkCells.c.

Function Documentation

void copyAtom	(	LinkCell *	boxes,
		Atoms *	atoms,
		int	iAtom,
		int	iBox,
		int	jAtom,
		int	jBox
	)

static

Copy atom iAtom in link cell iBox to atom jAtom in link cell jBox.

Any data at jAtom, jBox is overwritten. This routine can be used to re-order atoms within a link cell.

Definition at line 311 of file linkCells.c.

Here is the caller graph for this function:

void destroyLinkCells ( LinkCell ** boxes )

Definition at line 112 of file linkCells.c.

Here is the call graph for this function:

Here is the caller graph for this function:

void emptyHaloCells ( LinkCell * boxes )

static

Set the number of atoms to zero in all halo link cells.

Definition at line 368 of file linkCells.c.

Here is the caller graph for this function:

int getBoxFromCoord	(	LinkCell *	boxes,
		real_t	rr[3]
	)

static

Get the index of the link cell that contains the specified coordinate.

This can be either a halo or a local link cell.

Because the rank ownership of an atom is strictly determined by the atom's position, we need to take care that all ranks will agree which rank owns an atom. The conditionals at the end of this function are special care to ensure that all ranks make compatible link cell assignments for atoms that are near a link cell boundaries. If no ranks claim an atom in a local cell it will be lost. If multiple ranks claim an atom it will be duplicated.

Definition at line 333 of file linkCells.c.

Here is the call graph for this function:

Here is the caller graph for this function:

int getBoxFromTuple	(	LinkCell *	boxes,
		int	ix,
		int	iy,
		int	iz
	)

Calculates the link cell index from the grid coords.

The valid coordinate range in direction ii is [-1, gridSize[ii]]. Any coordinate that involves a -1 or gridSize[ii] is a halo link cell. Because of the order in which the local and halo link cells are stored the indices of the halo cells are special cases.

See Also: initLinkCells for an explanation of storage order.

Definition at line 189 of file linkCells.c.

Here is the caller graph for this function:

int getNeighborBoxes	(	LinkCell *	boxes,
		int	iBox,
		int *	nbrBoxes
	)

Populates the nbrBoxes array with the 27 boxes that are adjacent to iBox. The count is 27 instead of 26 because iBox is included in the list (as neighbor 13). Caller is responsible to alloc and free nbrBoxes.

Returns: The number of nbr boxes (always 27 in this implementation).

Definition at line 130 of file linkCells.c.

Here is the call graph for this function:

Here is the caller graph for this function:

void getTuple	(	LinkCell *	boxes,
		int	iBox,
		int *	ixp,
		int *	iyp,
		int *	izp
	)

static

Get the grid coordinates of the link cell with index iBox.

Local cells are easy as they use a standard 1D->3D mapping. Halo cell are special cases.

See Also: initLinkCells for information on link cell order.

Parameters

[in]	iBox	Index to link cell for which tuple is needed.
[out]	ixp	x grid coord of link cell.
[out]	iyp	y grid coord of link cell.
[out]	izp	z grid coord of link cell.

Definition at line 382 of file linkCells.c.

Here is the caller graph for this function:

LinkCell* initLinkCells	(	const Domain *	domain,
		real_t	cutoff
	)

In CoMD 1.1, atoms are stored in link cells.

Link cells are widely used in classical MD to avoid an O(N^2) search for atoms that interact. Link cells are formed by subdividing the local spatial domain with a Cartesian grid where the grid spacing in each direction is at least as big as he potential's cutoff distance. Because atoms don't interact beyond the potential cutoff, for an atom iAtom in any given link cell, we can be certain that all atoms that interact with iAtom are contained in the same link cell, or one of the 26 neighboring link cells.

CoMD chooses the link cell size (boxSize) on each axis to be the shortest possible distance, longer than cutoff, such that the local domain size divided by boxSize is an integer. I.e., the link cells are commensurate with with the local domain size. While this does not result in the smallest possible link cells, it does allow us to keep a strict separation between the link cells that are entirely inside the local domain and those that represent halo regions.

The number of local link cells in each direction is stored in gridSize. Local link cells have 3D grid coordinates (ix, iy, iz) where ix, iy, and iz can range from 0 to gridSize[iAxis]-1, whiere iAxis is 0 for x, 1 for y and 2 for the z direction. The number of local link cells is thus nLocalBoxes = gridSize[0]*gridSize[1]*gridSize[2].

The local link cells are surrounded by one complete shell of halo link cells. The halo cells provide temporary storage for halo or "ghost" atoms that belong to other tasks, but whose coordinates are needed locally to complete the force calculation. Halo link cells have at least one coordinate with a value of either -1 or gridSize[iAxis].

Because CoMD stores data in ordinary 1D C arrays, a mapping is needed from the 3D grid coords to a 1D array index. For the local cells we use the conventional mapping ix + iy*nx + iz*nx*ny. This keeps all of the local cells in a contiguous region of memory starting from the beginning of any relevant array and makes it easy to iterate the local cells in a single loop. Halo cells are mapped differently. After the local cells, the two planes of link cells that are face neighbors with local cells across the -x or +x axis are next. These are followed by face neighbors across the -y and +y axis (including cells that are y-face neighbors with an x-plane of halo cells), followed by all remaining cells in the -z and +z planes of halo cells. The total number of link cells (on each rank) is nTotalBoxes.

Data storage arrays that are used in association with link cells should be allocated to store nTotalBoxes*MAXATOMS items. Data for the first atom in linkCell iBox is stored at index iBox*MAXATOMS. Data for subsequent atoms in the same link cell are stored sequentially, and the number of atoms in link cell iBox is nAtoms[iBox].

See Also: getBoxFromTuple is the 3D->1D mapping for link cell indices.; getTuple is the 1D->3D mapping

Parameters

[in] cutoff The cutoff distance of the potential.

Definition at line 82 of file linkCells.c.

Here is the call graph for this function:

Here is the caller graph for this function:

int maxOccupancy ( LinkCell * boxes )

Returns: The largest number of atoms in any link cell.

Definition at line 293 of file linkCells.c.

Here is the call graph for this function:

Here is the caller graph for this function:

void moveAtom	(	LinkCell *	boxes,
		Atoms *	atoms,
		int	iId,
		int	iBox,
		int	jBox
	)

Move an atom from one link cell to another.

Parameters

iId	[in] The index with box iBox of the atom to be moved.
iBox	[in] The index of the link cell the particle is moving from.
jBox	[in] The index of the link cell the particle is moving to.

Definition at line 242 of file linkCells.c.

Here is the call graph for this function:

Here is the caller graph for this function:

void putAtomInBox	(	LinkCell *	boxes,
		Atoms *	atoms,
		const int	gid,
		const int	iType,
		const real_t	x,
		const real_t	y,
		const real_t	z,
		const real_t	px,
		const real_t	py,
		const real_t	pz
	)

Finds the appropriate link cell for an atom based on the spatial coordinates and stores data in that link cell.

Parameters

[in]	gid	The global of the atom.
[in]	iType	The species index of the atom.
[in]	x	The x-coordinate of the atom.
[in]	y	The y-coordinate of the atom.
[in]	z	The z-coordinate of the atom.
[in]	px	The x-component of the atom's momentum.
[in]	py	The y-component of the atom's momentum.
[in]	pz	The z-component of the atom's momentum.

Definition at line 155 of file linkCells.c.

Here is the call graph for this function:

Here is the caller graph for this function:

void updateLinkCells	(	LinkCell *	boxes,
		Atoms *	atoms
	)

Update link cell data structures when the atoms have moved.

This is the first step in returning data structures to a consistent state after the atoms move each time step. First we discard all atoms in the halo link cells. These are all atoms that are currently stored on other ranks and so any information we have about them is stale. Next, we move any atoms that have crossed link cell boundaries into their new link cells. It is likely that some atoms will be moved into halo link cells. Since we have deleted halo atoms from other tasks, it is clear that any atoms that are in halo cells at the end of this routine have just transitioned from local to halo atoms. Such atom must be sent to other tasks by a halo exchange to avoid being lost.

See Also: redistributeAtoms

Definition at line 273 of file linkCells.c.

Here is the call graph for this function:

Here is the caller graph for this function:

Macros

Functions

Detailed Description

Macro Definition Documentation

Function Documentation