Inheritance diagram for OpenMD::ForceMatrixDecomposition:

Public Member Functions
	ForceMatrixDecomposition (SimInfo info, InteractionManager iMan)

void	distributeInitialData ()
	distributeInitialData is essentially a copy of the older fortran SimulationSetup

void	zeroWorkArrays ()

void	distributeData ()

void	collectIntermediateData ()

void	distributeIntermediateData ()

void	collectSelfData ()
	Collects information obtained during the post-pair (and embedding functional) loops onto local data structures.

void	collectData ()

void	buildNeighborList (vector< int > &neighborList, vector< int > &point, vector< Vector3d > &savedPositions)

Vector3d &	getGroupVelocityColumn (int cg2)

vector< int > &	getAtomsInGroupRow (int cg1)
	returns the list of atoms belonging to this group.

vector< int > &	getAtomsInGroupColumn (int cg2)

Vector3d	getAtomToGroupVectorRow (int atom1, int cg1)

Vector3d	getAtomToGroupVectorColumn (int atom2, int cg2)

RealType &	getMassFactorRow (int atom1)

RealType &	getMassFactorColumn (int atom2)

Vector3d	getIntergroupVector (int cg1, int cg2)

Vector3d	getInteratomicVector (int atom1, int atom2)

int &	getNAtomsInRow ()

int	getTopologicalDistance (int atom1, int atom2)

vector< int > &	getExcludesForAtom (int atom1)

bool	skipAtomPair (int atom1, int atom2, int cg1, int cg2)
	We need to exclude some overcounted interactions that result from the parallel decomposition.

bool	excludeAtomPair (int atom1, int atom2)
	We need to handle the interactions for atoms who are involved in the same rigid body as well as some short range interactions (bonds, bends, torsions) differently from other interactions.

int	getGlobalIDRow (int atom1)

int	getGlobalIDCol (int atom1)

int	getGlobalID (int atom1)

void	addForceToAtomRow (int atom1, Vector3d fg)

void	addForceToAtomColumn (int atom2, Vector3d fg)

Vector3d &	getAtomVelocityColumn (int atom2)

void	fillInteractionData (InteractionData &idat, int atom1, int atom2, bool newAtom1=true)

void	unpackInteractionData (InteractionData &idat, int atom1, int atom2)

void	unpackPrePairData (InteractionData &idat, int atom1, int atom2)

Public Member Functions inherited from OpenMD::ForceDecomposition
	ForceDecomposition (SimInfo info, InteractionManager iMan)

virtual void	setSnapshot (Snapshot *snap)

virtual potVec	getSelfPotential ()

virtual potVec	getPairwisePotential ()

virtual potVec	getExcludedPotential ()

virtual potVec	getSelectedPotential ()

virtual potVec	getExcludedSelfPotential ()

virtual potVec	getSelectedSelfPotential ()

virtual bool	checkNeighborList (vector< Vector3d > savedPositions)

void	setCutoffRadius (RealType rCut)

virtual void	fillSelfData (SelfData &sdat, int atom)

virtual void	unpackSelfData (SelfData &sdat, int atom)

virtual void	fillPreForceData (SelfData &sdat, int atom)

virtual void	unpackPreForceData (SelfData &sdat, int atom)

virtual void	addToHeatFlux (Vector3d hf)

virtual void	setHeatFlux (Vector3d hf)

Public Attributes
vector< int >	cgRowToGlobal

vector< int >	cgColToGlobal

Additional Inherited Members
Protected Attributes inherited from OpenMD::ForceDecomposition
SimInfo *	info_ {nullptr}

SnapshotManager *	sman_

Snapshot *	snap_

ForceField *	ff_

InteractionManager *	interactionMan_

int	atomStorageLayout_

int	rigidBodyStorageLayout_

int	cutoffGroupStorageLayout_

bool	needVelocities_

bool	usePeriodicBoundaryConditions_

RealType	skinThickness_
	Verlet neighbor list skin thickness.

RealType	rCut_

RealType	rList_

RealType	rListSq_

vector< int >	idents

vector< int >	regions

potVec	pairwisePot

potVec	selfPot

potVec	excludedPot

potVec	excludedSelfPot

potVec	selectedPot

potVec	selectedSelfPot

vector< vector< int > >	toposForAtom
	The topological distance between two atomic sites is handled via two vector structures for speed.

vector< vector< int > >	topoDist

vector< vector< int > >	excludesForAtom

vector< vector< int > >	groupList_

vector< RealType >	massFactors

vector< AtomType * >	atypesLocal

vector< Vector3i >	cellOffsets_

Vector3i	nCells_

vector< vector< int > >	cellList_

Detailed Description

Definition at line 59 of file ForceMatrixDecomposition.hpp.

Constructor & Destructor Documentation

◆ ForceMatrixDecomposition()

OpenMD::ForceMatrixDecomposition::ForceMatrixDecomposition	(	SimInfo *	info,
		InteractionManager *	iMan )

Definition at line 54 of file ForceMatrixDecomposition.cpp.

◆ ~ForceMatrixDecomposition()

OpenMD::ForceMatrixDecomposition::~ForceMatrixDecomposition ( )

Definition at line 88 of file ForceMatrixDecomposition.cpp.

Member Function Documentation

◆ addForceToAtomColumn()

void OpenMD::ForceMatrixDecomposition::addForceToAtomColumn	(	int	atom2,
		Vector3d	fg )

virtual

Implements OpenMD::ForceDecomposition.

Definition at line 979 of file ForceMatrixDecomposition.cpp.

◆ addForceToAtomRow()

void OpenMD::ForceMatrixDecomposition::addForceToAtomRow	(	int	atom1,
		Vector3d	fg )

virtual

Implements OpenMD::ForceDecomposition.

Definition at line 971 of file ForceMatrixDecomposition.cpp.

◆ buildNeighborList()

void OpenMD::ForceMatrixDecomposition::buildNeighborList	(	vector< int > &	neighborList,
		vector< int > &	point,
		vector< Vector3d > &	savedPositions )

virtual

Implements OpenMD::ForceDecomposition.

Definition at line 1333 of file ForceMatrixDecomposition.cpp.

◆ collectData()

void OpenMD::ForceMatrixDecomposition::collectData ( )

virtual

Implements OpenMD::ForceDecomposition.

Definition at line 576 of file ForceMatrixDecomposition.cpp.

◆ collectIntermediateData()

void OpenMD::ForceMatrixDecomposition::collectIntermediateData ( )

virtual

Implements OpenMD::ForceDecomposition.

Definition at line 520 of file ForceMatrixDecomposition.cpp.

◆ collectSelfData()

void OpenMD::ForceMatrixDecomposition::collectSelfData ( )

virtual

Collects information obtained during the post-pair (and embedding functional) loops onto local data structures.

Implements OpenMD::ForceDecomposition.

Definition at line 783 of file ForceMatrixDecomposition.cpp.

◆ distributeData()

void OpenMD::ForceMatrixDecomposition::distributeData ( )

virtual

Implements OpenMD::ForceDecomposition.

Definition at line 456 of file ForceMatrixDecomposition.cpp.

◆ distributeInitialData()

void OpenMD::ForceMatrixDecomposition::distributeInitialData ( )

virtual

distributeInitialData is essentially a copy of the older fortran SimulationSetup

Implements OpenMD::ForceDecomposition.

Definition at line 111 of file ForceMatrixDecomposition.cpp.

References OpenMD::ForceField::getAtomType(), OpenMD::SnapshotManager::getCurrentSnapshot(), OpenMD::SimInfo::getForceField(), OpenMD::SimInfo::getGlobalAtomIndices(), OpenMD::SimInfo::getGlobalGroupIndices(), OpenMD::SimInfo::getNLocalCutoffGroups(), OpenMD::Snapshot::getNumberOfAtoms(), OpenMD::PairList::hasPair(), OpenMD::DataStorage::resize(), OpenMD::DataStorage::setStorageLayout(), and OpenMD::ForceDecomposition::toposForAtom.

◆ distributeIntermediateData()

void OpenMD::ForceMatrixDecomposition::distributeIntermediateData ( )

virtual

Implements OpenMD::ForceDecomposition.

Definition at line 555 of file ForceMatrixDecomposition.cpp.

◆ excludeAtomPair()

bool OpenMD::ForceMatrixDecomposition::excludeAtomPair	(	int	atom1,
		int	atom2 )

virtual

We need to handle the interactions for atoms who are involved in the same rigid body as well as some short range interactions (bonds, bends, torsions) differently from other interactions.

We'll still visit the pairwise routines, but with a flag that tells those routines to exclude the pair from direct long range interactions. Some indirect interactions (notably reaction field) must still be handled for these pairs.

Implements OpenMD::ForceDecomposition.

Definition at line 959 of file ForceMatrixDecomposition.cpp.