Neighbor lists and spatial decomposition. More...

Classes
struct	tinker::EnableEnumBitMask< Nbl >

struct	tinker::NBList
	Verlet list: pairwise neighbor list indices and storage. More...

class	tinker::Spatial

struct	tinker::Spatial::SortedAtom

struct	tinker::Spatial::Center

struct	tinker::Spatial::ScaleInfo

Typedefs
typedef GenericUnit< NBList, GenericUnitVersion::ENABLE_ON_DEVICE >	tinker::NBListUnit

typedef GenericUnit< Spatial, GenericUnitVersion::DISABLE_ON_DEVICE >	tinker::SpatialUnit

Enumerations
enum class	tinker::Nbl { tinker::Nbl::UNDEFINED = 0x00 , tinker::Nbl::DOUBLE_LOOP = 0x01 , tinker::Nbl::VERLET = 0x02 , tinker::Nbl::SPATIAL = 0x04 }

Functions
Nbl	tinker::vlistVersion ()

Nbl	tinker::clistVersion ()

Nbl	tinker::mlistVersion ()
	For multipole, polarization, repulsion, etc. More...

Nbl	tinker::ulistVersion ()
	For sparse preconditioner. More...

Nbl	tinker::dsplistVersion ()
	For dispersion. More...

void	tinker::nblistData (RcOp)
	Sets up data on device. More...

void	tinker::nblistRefresh ()
	Updates the neighbor lists. More...

void	tinker::spatialUpdate (SpatialUnit)

Detailed Description

Neighbor lists and spatial decomposition.

Class Documentation

◆ tinker::EnableEnumBitMask< Nbl >

struct tinker::EnableEnumBitMask< Nbl >

Static Public Attributes
static constexpr bool	value = true

Member Data Documentation

◆ value

constexpr bool tinker::EnableEnumBitMask< Nbl >::value = true

staticconstexpr

◆ tinker::NBList

struct tinker::NBList

Verlet list: pairwise neighbor list indices and storage.

Public Member Functions
	~NBList ()

Public Attributes
int *	nlst
	number of sites in list for each atom More...

int *	lst
	all of the sites in list More...

int *	update
	update flag for each atom More...

real *	xold
	old x coordinates More...

real *	yold
	old y coordinates More...

real *	zold
	old z coordinates More...

const real *	x
	current x coordinates More...

const real *	y
	current y coordinates More...

const real *	z
	current z coordinates More...

int	maxnlst
	max number of neighbors for each atom More...

real	cutoff
	list cutoff distance More...

real	buffer
	width of the neighbor list buffer region More...

Constructor & Destructor Documentation

◆ ~NBList()

tinker::NBList::~NBList ( )

Member Data Documentation

◆ buffer

real tinker::NBList::buffer

width of the neighbor list buffer region

◆ cutoff

real tinker::NBList::cutoff

list cutoff distance

◆ lst

int* tinker::NBList::lst

all of the sites in list

◆ maxnlst

int tinker::NBList::maxnlst

max number of neighbors for each atom

◆ nlst

int* tinker::NBList::nlst

number of sites in list for each atom

◆ update

int* tinker::NBList::update

update flag for each atom

◆ x

const real* tinker::NBList::x

current x coordinates

◆ xold

real* tinker::NBList::xold

old x coordinates

◆ y

const real* tinker::NBList::y

current y coordinates

◆ yold

real* tinker::NBList::yold

old y coordinates

◆ z

const real* tinker::NBList::z

current z coordinates

◆ zold

real* tinker::NBList::zold

old z coordinates

◆ tinker::Spatial

class tinker::Spatial

Public Member Functions
	~Spatial ()

Static Public Member Functions
static void	dataAlloc (SpatialUnit &u, int n, double cutoff, double buffer, const real x, const real y, const real z, int nstype, int ns1, int(js1)[2], int ns2, int(js2)[2], int ns3, int(js3)[2], int ns4, int(*js4)[2])

static void	dataInit (SpatialUnit)

static void	dataUpdateSorted (SpatialUnit)

template<class IMG >
static void	RunStep5 (SpatialUnit u)

Public Attributes
ScaleInfo	si1
	#ScaleInfo object 1. More...

ScaleInfo	si2
	#ScaleInfo object 2. More...

ScaleInfo	si3
	#ScaleInfo object 3. More...

ScaleInfo	si4
	#ScaleInfo object 4. More...

SortedAtom *	sorted
	Sorted atoms. Length n. More...

int *	bnum
	`bnum[sorted[i].unsorted] = i`. Length n. More...

Center *	akc

Center *	half
	Half box size and radius. Length nak. More...

int *	iakpl

int *	lst

int *	iak

const real *	x
	Reference of the coordinates. More...

const real *	y
	Reference of the coordinates. More...

const real *	z
	Reference of the coordinates. More...

int *	update

real	cutoff
	Cutoff distance. More...

real	buffer
	Cutoff buffer distance. More...

int	fresh

int	nakpl
	Length of iakpl. Multiple. More...

int	niak
	Length of iak, not greater than LSTCAP*nak. More...

int	n
	Number of atoms. More...

Static Public Attributes
static constexpr int	BLOCK = 32

static constexpr int	LSTCAP = 48
	Parameter for pre-allocating work arrays. More...

Friends
void	nblistRefresh ()
	Updates the neighbor lists. More...

void	spatialUpdate (SpatialUnit)

void	spatialDataInit_cu (SpatialUnit)

Constructor & Destructor Documentation

◆ ~Spatial()

tinker::Spatial::~Spatial ( )

Member Function Documentation

◆ dataAlloc()

static void tinker::Spatial::dataAlloc	(	SpatialUnit &	u,
		int	n,
		double	cutoff,
		double	buffer,
		const real *	x,
		const real *	y,
		const real *	z,
		int	nstype,
		int	ns1,
		int(*)	js1[2],
		int	ns2,
		int(*)	js2[2],
		int	ns3,
		int(*)	js3[2],
		int	ns4,
		int(*)	js4[2]
	)

static

◆ dataInit()

static void tinker::Spatial::dataInit ( SpatialUnit )

static

◆ dataUpdateSorted()

static void tinker::Spatial::dataUpdateSorted ( SpatialUnit )

static

◆ RunStep5()

template<class IMG >

static void tinker::Spatial::RunStep5 ( SpatialUnit u )

static

Friends And Related Function Documentation

◆ nblistRefresh

void nblistRefresh ( )

friend

Updates the neighbor lists.

◆ spatialDataInit_cu

void spatialDataInit_cu ( SpatialUnit )

friend

◆ spatialUpdate

void spatialUpdate ( SpatialUnit )

friend

Member Data Documentation

◆ akc

Center* tinker::Spatial::akc

Block centers and the logical flag for a centralized block of atoms. Length nak.

◆ BLOCK

constexpr int tinker::Spatial::BLOCK = 32

staticconstexpr

Number of atom per block. Equal to WARP_SIZE and sizeof(int).

◆ bnum

int* tinker::Spatial::bnum

bnum[sorted[i].unsorted] = i. Length n.

◆ buffer

real tinker::Spatial::buffer

Cutoff buffer distance.

◆ cutoff

real tinker::Spatial::cutoff

Cutoff distance.

◆ fresh

int tinker::Spatial::fresh

Logical flag for a fresh neighbor list, meaning no changes in the coordinates after the list construction.

◆ half

Center* tinker::Spatial::half

Half box size and radius. Length nak.

◆ iak

int* tinker::Spatial::iak

Block numbers Bi. Every Bi is duplicated several times to match its padded neighbors in lst. One Bi corresponds to BLOCK neighbors.

◆ iakpl

int* tinker::Spatial::iakpl

List of block pairs subject to exclusion rules. Length nakpl. The pair (x,y) was encoded via triangular number and stored as tri(x)+y.

◆ lst

int* tinker::Spatial::lst

Neighbors of a block of atoms. For a pair (Bi,Nij), Nij is the j-th neighbor of atoms in block Bi. These neighbors of Bi are padded with impossible atom number to make the count of Nij a multiple of BLOCK.

◆ LSTCAP

constexpr int tinker::Spatial::LSTCAP = 48

staticconstexpr

Parameter for pre-allocating work arrays.

◆ n

int tinker::Spatial::n

Number of atoms.

◆ nakpl

int tinker::Spatial::nakpl

Length of iakpl. Multiple.

◆ niak

int tinker::Spatial::niak

Length of iak, not greater than LSTCAP*nak.

◆ si1

ScaleInfo tinker::Spatial::si1

#ScaleInfo object 1.

◆ si2

ScaleInfo tinker::Spatial::si2

#ScaleInfo object 2.

◆ si3

ScaleInfo tinker::Spatial::si3

#ScaleInfo object 3.

◆ si4

ScaleInfo tinker::Spatial::si4

#ScaleInfo object 4.

◆ sorted

SortedAtom* tinker::Spatial::sorted

Sorted atoms. Length n.

◆ update

int* tinker::Spatial::update

Work array of length max(2*#n,128). One use is to store the logical flags during the list update.

◆ x

const real* tinker::Spatial::x

Reference of the coordinates.

◆ y

const real* tinker::Spatial::y

Reference of the coordinates.

◆ z

const real* tinker::Spatial::z

Reference of the coordinates.

◆ tinker::Spatial::SortedAtom

struct tinker::Spatial::SortedAtom

Sorted atoms.

Public Attributes
real	x

real	y

real	z

int	unsorted
	Original atom number. More...

Member Data Documentation

◆ unsorted

int tinker::Spatial::SortedAtom::unsorted

Original atom number.

◆ x

real tinker::Spatial::SortedAtom::x

◆ y

real tinker::Spatial::SortedAtom::y

◆ z

real tinker::Spatial::SortedAtom::z

◆ tinker::Spatial::Center

struct tinker::Spatial::Center

Public Attributes
real	x

real	y

real	z

real	w

Member Data Documentation

◆ w

real tinker::Spatial::Center::w

◆ x

real tinker::Spatial::Center::x

◆ y

real tinker::Spatial::Center::y

◆ z

real tinker::Spatial::Center::z

◆ tinker::Spatial::ScaleInfo

struct tinker::Spatial::ScaleInfo

Public Member Functions
void	init ()

void	set (int nns, int(*jjs)[2])

Public Attributes
int(*	js )[2]
	Atom pairs of atoms with exclusion rules (of length ns). More...

unsigned int *	bit0

int	ns
	Number of pairs of atoms with exclusion rules. More...

Member Function Documentation

◆ init()

void tinker::Spatial::ScaleInfo::init ( )

◆ set()

void tinker::Spatial::ScaleInfo::set	(	int	nns,
		int(*)	jjs[2]
	)

Member Data Documentation

◆ bit0

unsigned int* tinker::Spatial::ScaleInfo::bit0

Bits array, stored as 32-bit unsigned integers (of length 32*cap_nakpl).

◆ js

int(* tinker::Spatial::ScaleInfo::js)[2]

Atom pairs of atoms with exclusion rules (of length ns).

◆ ns

int tinker::Spatial::ScaleInfo::ns

Number of pairs of atoms with exclusion rules.

Typedef Documentation

◆ NBListUnit

typedef GenericUnit<NBList, GenericUnitVersion::ENABLE_ON_DEVICE> tinker::NBListUnit

◆ SpatialUnit

typedef GenericUnit<Spatial, GenericUnitVersion::DISABLE_ON_DEVICE> tinker::SpatialUnit

Enumeration Type Documentation

◆ Nbl

enum class tinker::Nbl

strong

Enumerator
UNDEFINED	Undefined.
DOUBLE_LOOP	Double loop.
VERLET	Verlet neighbor list.
SPATIAL	Spatial decomposition.

Function Documentation

◆ clistVersion()

Nbl tinker::clistVersion ( )

For partial charge models and for VDW models that do not have a separate set of coordinates.

◆ dsplistVersion()

Nbl tinker::dsplistVersion ( )

For dispersion.

◆ mlistVersion()

Nbl tinker::mlistVersion ( )

For multipole, polarization, repulsion, etc.

◆ nblistData()

void tinker::nblistData ( RcOp )

Sets up data on device.

◆ nblistRefresh()

void tinker::nblistRefresh ( )

Updates the neighbor lists.

◆ spatialUpdate()

void tinker::spatialUpdate ( SpatialUnit )

◆ ulistVersion()

Nbl tinker::ulistVersion ( )

For sparse preconditioner.

◆ vlistVersion()

Nbl tinker::vlistVersion ( )

For Halgren Buffered 14-7 potential only, otherwise returns Nbl::UNDEFINED.

Variable Documentation

◆ clist_unit

NBListUnit tinker::clist_unit

extern

◆ cspatial_fresh_mask_echglj

constexpr int tinker::cspatial_fresh_mask_echglj = 0x00000001

constexpr

◆ cspatial_v2_unit

SpatialUnit tinker::cspatial_v2_unit

extern

◆ dsplist_unit

NBListUnit tinker::dsplist_unit

extern

◆ dspspatial_v2_unit

SpatialUnit tinker::dspspatial_v2_unit

extern

◆ mlist_unit

NBListUnit tinker::mlist_unit

extern

◆ mspatial_v2_unit

SpatialUnit tinker::mspatial_v2_unit

extern

◆ ulist_unit

NBListUnit tinker::ulist_unit

extern

◆ uspatial_v2_unit

SpatialUnit tinker::uspatial_v2_unit

extern

◆ vlist_unit

NBListUnit tinker::vlist_unit

extern

◆ vspatial_v2_unit

SpatialUnit tinker::vspatial_v2_unit

extern

Variables
NBListUnit	tinker::vlist_unit

NBListUnit	tinker::clist_unit

NBListUnit	tinker::mlist_unit

NBListUnit	tinker::ulist_unit

NBListUnit	tinker::dsplist_unit

SpatialUnit	tinker::cspatial_v2_unit

SpatialUnit	tinker::vspatial_v2_unit

SpatialUnit	tinker::uspatial_v2_unit

SpatialUnit	tinker::mspatial_v2_unit

SpatialUnit	tinker::dspspatial_v2_unit

constexpr int	tinker::cspatial_fresh_mask_echglj = 0x00000001

Classes

Typedefs

Enumerations

Functions

Variables

Detailed Description

Class Documentation

◆ tinker::EnableEnumBitMask< Nbl >

Static Public Attributes

Member Data Documentation

◆ value

◆ tinker::NBList

Public Member Functions

Public Attributes

Constructor & Destructor Documentation

◆ ~NBList()

Member Data Documentation

◆ buffer

◆ cutoff

◆ lst

◆ maxnlst

◆ nlst

◆ update

◆ x

◆ xold

◆ y

◆ yold

◆ z

◆ zold

◆ tinker::Spatial

Public Member Functions

Static Public Member Functions

Public Attributes

Static Public Attributes

Friends

Constructor & Destructor Documentation

◆ ~Spatial()

Member Function Documentation

◆ dataAlloc()

◆ dataInit()

◆ dataUpdateSorted()

◆ RunStep5()

Friends And Related Function Documentation

◆ nblistRefresh

◆ spatialDataInit_cu

◆ spatialUpdate

Member Data Documentation

◆ akc

◆ BLOCK

◆ bnum

◆ buffer

◆ cutoff

◆ fresh

◆ half

◆ iak

◆ iakpl

◆ lst

◆ LSTCAP

◆ n

◆ nakpl

◆ niak

◆ si1

◆ si2

◆ si3

◆ si4

◆ sorted

◆ update

◆ x

◆ y

◆ z

◆ tinker::Spatial::SortedAtom

Public Attributes

Member Data Documentation

◆ unsorted

◆ x

◆ y

◆ z

◆ tinker::Spatial::Center

Public Attributes

Member Data Documentation