Custom bond class (not to be confused with a LAMMPS bond). More...

#include <bond.h>

Public Member Functions
	Bond ()

	Bond (const LAMMPS_NS::tagint &bond_atom_in, const int &bond_type_in, const bool &head_parent_atom_in)

	~Bond ()

const LAMMPS_NS::tagint &	getBondAtom () const

const int &	getBondType () const

bool	parentAtomIsHead () const
	For each bond in the system a tail and a head atom are (randomly) defined. This prevents the discovery of identical (i.e., defined twice) PAPRECA::BondBreak events. More...

void	assignBondAtom (const LAMMPS_NS::tagint &bond_atom_in)

void	assignBondType (const int &bond_type_in)

Static Public Member Functions
static const bool	atomIDIsMapped (LAMMPS_NS::tagint &parent_atomID, ATOM2BONDS_MAP &atomID2bonds)

static void	addBond2BondVector (int &bond_type, LAMMPS_NS::tagint &parent_atomID, LAMMPS_NS::tagint &bond_atomID, const bool &head_atom_parent, ATOM2BONDS_MAP &atomID2bonds)

static void	fillAtomID2BondsContainer (ATOM2BONDS_MAP &atomID2bonds, LAMMPS_NS::tagint *bonds_list, const LAMMPS_NS::bigint &bonds_num)

static void	initAtomID2BondsMap (LAMMPS_NS::LAMMPS *lmp, const int &proc_id, ATOM2BONDS_MAP &atomID2bonds)

static bool	atomHasBonds (const LAMMPS_NS::tagint &iatom_id, ATOM2BONDS_MAP &atomID2bonds)

static void	recursiveCollectBondedAtoms (LAMMPS_NS::tagint &atom_id, std::vector< LAMMPS_NS::tagint > &delids_local, TAGINT_SET &delids_set, ATOM2BONDS_MAP &atomID2bonds)

Private Attributes
LAMMPS_NS::tagint	bond_atom = -1

int	bond_type = -1

bool	head_parent_atom = false

Detailed Description

Custom bond class (not to be confused with a LAMMPS bond).

Every atom in the system is associated with a vector of bond objects. The bonds vector of objects provides easy access to bonded atom IDs and bond types. PAPRECA::Bond objects enable bond formation, bond breaking, and custom diffusion events (e.g., the Fe_4PO4neib diffusion style deploys the bond vectors of the neighbors of the candidate Fe atom to determine whether or not there are 4 PO4 in the parent Fe neighborhood). The unordered_map PAPRECA::ATOM2BONDS_MAP can be used to retrieve the relevant vector of bond objects using a LAMMPS atom ID.

Constructor & Destructor Documentation

◆ Bond() [1/2]

PAPRECA::Bond::Bond ( )

◆ Bond() [2/2]

PAPRECA::Bond::Bond	(	const LAMMPS_NS::tagint &	bond_atom_in,
		const int &	bond_type_in,
		const bool &	head_parent_atom_in
	)

◆ ~Bond()

PAPRECA::Bond::~Bond ( )

Member Function Documentation

◆ addBond2BondVector()

void PAPRECA::Bond::addBond2BondVector	(	int &	bond_type,
		LAMMPS_NS::tagint &	parent_atomID,
		LAMMPS_NS::tagint &	bond_atomID,
		const bool &	head_atom_parent,
		ATOM2BONDS_MAP &	atomID2bonds
	)

static

Receives the bond type and atom IDs of a bond. Then, initializes a PAPRECA::Bond and inserts it in the relevant std::vector< PAPRECA::Bond > containers. The std::vector< PAPRECA::Bond > containers are stored in the atomID2bonds map.

Parameters

[in]	bond_type	type of bond.
[in]	parent_atomID	ID of the first atom ID of the bond.
[in]	bond_atomID	ID of the second atom ID of the bond.
[in]	head_atom_parent	boolean dictating whether the parent_atomID is the head atom of the current bond
[in,out]	atomID2bonds	PAPRECA::ATOM2BONDS_MAP container (i.e., std::unordered_map< LAMMPS_NS::tagint parent_atomID , std::vector< PAPRECA::Bond > >). The atomID2bonds container provides direct access to all the bonds of the parent atom.

See also: PAPRECA::Bond::fillAtomID2BondsContainer(), PAPRECA::Bond::initAtomID2BondsMap(), PAPRECA::Bond::atomIDIsMapped(), PAPRECA::Bond::initAndGatherBondsList()

◆ assignBondAtom()

void PAPRECA::Bond::assignBondAtom ( const LAMMPS_NS::tagint & bond_atom_in )

◆ assignBondType()

void PAPRECA::Bond::assignBondType ( const int & bond_type_in )

◆ atomHasBonds()

bool PAPRECA::Bond::atomHasBonds	(	const LAMMPS_NS::tagint &	iatom_id,
		ATOM2BONDS_MAP &	atomID2bonds
	)

static

◆ atomIDIsMapped()

const bool PAPRECA::Bond::atomIDIsMapped	(	LAMMPS_NS::tagint &	parent_atomID,
		PAPRECA::ATOM2BONDS_MAP &	atomID2bonds
	)

static

Checks if the parent_atomID is contained in the atomID2bonds map

Parameters

[in]	parent_atomID	ID of parent atom.
[in]	atomID2bonds	PAPRECA::ATOM2BONDS_MAP container (i.e., std::unordered_map< LAMMPS_NS::tagint parent_atomID , std::vector< PAPRECA::Bond > >). The atomID2bonds container provides direct access to all the bonds of the parent atom.

See also: PAPRECA::Bond::fillAtomID2BondsContainer(), PAPRECA::Bond::addBond2BondVector(), PAPRECA::Bond::initAtomID2BondsMap(), PAPRECA::Bond::initAndGatherBondsList()

◆ fillAtomID2BondsContainer()

void PAPRECA::Bond::fillAtomID2BondsContainer	(	ATOM2BONDS_MAP &	atomID2bonds,
		LAMMPS_NS::tagint *	bonds_list,
		const LAMMPS_NS::bigint &	bonds_num
	)

static

Fills atomID2bonds container with bonds gathered from LAMMPS and stored in the bonds_list array.

Parameters

[in,out]	atomID2bonds	PAPRECA::ATOM2BONDS_MAP container (i.e., std::unordered_map< LAMMPS_NS::tagint parent_atomID , std::vector< PAPRECA::Bond > >). The atomID2bonds container provides direct access to all the bonds of the parent atom.
[in]	bonds_list	array containing the IDs of bonds.
[in]	bonds_num	number of bonds in the bonds_list array.

See also: PAPRECA::Bond::initAtomID2BondsMap(), PAPRECA::Bond::addBond2BondVector(), PAPRECA::Bond::atomIDIsMapped(), PAPRECA::Bond::initAndGatherBondsList()

◆ getBondAtom()

const LAMMPS_NS::tagint & PAPRECA::Bond::getBondAtom ( ) const

◆ getBondType()

const int & PAPRECA::Bond::getBondType ( ) const

◆ initAtomID2BondsMap()

void PAPRECA::Bond::initAtomID2BondsMap	(	LAMMPS_NS::LAMMPS *	lmp,
		const int &	proc_id,
		ATOM2BONDS_MAP &	atomID2bonds
	)

static

Initializes/fills atomID2bonds map. This is done by 1) gathering all bonds from the LAMMPS instance, 2) creating a std::vector< PAPRECA::Bond > container for each atomID, 3) filling the std::vector< PAPRECA::Bond > container with the IDs of bonded atoms.

Parameters

[in]	lmp	pointer to LAMMPS object.
[in]	proc_id	ID of current MPI process.
[in,out]	atomID2bonds	PAPRECA::ATOM2BONDS_MAP container (i.e., std::unordered_map< LAMMPS_NS::tagint parent_atomID , std::vector< PAPRECA::Bond > >). The atomID2bonds container provides direct access to all the bonds of the parent atom.

See also: PAPRECA::Bond::fillAtomID2BondsContainer(), PAPRECA::Bond::addBond2BondVector(), PAPRECA::Bond::atomIDIsMapped(), PAPRECA::Bond::initAndGatherBondsList()

◆ parentAtomIsHead()

bool PAPRECA::Bond::parentAtomIsHead ( ) const

For each bond in the system a tail and a head atom are (randomly) defined. This prevents the discovery of identical (i.e., defined twice) PAPRECA::BondBreak events.

◆ recursiveCollectBondedAtoms()

void PAPRECA::Bond::recursiveCollectBondedAtoms	(	LAMMPS_NS::tagint &	atom_id,
		std::vector< LAMMPS_NS::tagint > &	delids_local,
		TAGINT_SET &	delids_set,
		ATOM2BONDS_MAP &	atomID2bonds
	)

static

Recursively collects all bonded atoms of an atom. The IDs of collected atoms are inserted in the std::vector< tagint > container (delids_local). The vector of PAPRECA::Bond objects is retrieved for the atom_id from the atomID2bonds map. The function uses an atom tagint to start adding bonded atoms and returns when all bonded atoms are recursively collected (uses an std::unordered_set to decide that).

Parameters

[in]	atom_id	ID of atom.
[in,out]	delids_local	vector of collected atom IDs.
[in,out]	delids_set	std::unordered_set< LAMMPS_NS::tagint > containing atom IDs marked for deletion. Used to avoid duplicate deletion of atoms.
[in]	atomID2bonds	PAPRECA::ATOM2BONDS_MAP container (i.e., std::unordered_map< LAMMPS_NS::tagint parent_atomID , std::vector< PAPRECA::Bond > >). The atomID2bonds container provides direct access to all the bonds of the parent atom.

Note: This function works consistently because all MPI processes contain the same data in their atomID2bonds map.

See also: PAPRECA::Bond::initAtomID2BondsMap()

Member Data Documentation

◆ bond_atom

LAMMPS_NS::tagint PAPRECA::Bond::bond_atom = -1

private

◆ bond_type

int PAPRECA::Bond::bond_type = -1

private

◆ head_parent_atom

bool PAPRECA::Bond::head_parent_atom = false

private

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

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Bond() [1/2]

◆ Bond() [2/2]

◆ ~Bond()

Member Function Documentation

◆ addBond2BondVector()

◆ assignBondAtom()

◆ assignBondType()

◆ atomHasBonds()

◆ atomIDIsMapped()

◆ fillAtomID2BondsContainer()

◆ getBondAtom()

◆ getBondType()

◆ initAtomID2BondsMap()

◆ parentAtomIsHead()

◆ recursiveCollectBondedAtoms()

Member Data Documentation

◆ bond_atom

◆ bond_type

◆ head_parent_atom