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 62 of file ForceMatrixDecomposition.hpp.

Constructor & Destructor Documentation

◆ ForceMatrixDecomposition()

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

Definition at line 57 of file ForceMatrixDecomposition.cpp.

◆ ~ForceMatrixDecomposition()

OpenMD::ForceMatrixDecomposition::~ForceMatrixDecomposition ( )

Definition at line 91 of file ForceMatrixDecomposition.cpp.

Member Function Documentation

◆ addForceToAtomColumn()

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

virtual

Implements OpenMD::ForceDecomposition.

Definition at line 982 of file ForceMatrixDecomposition.cpp.

◆ addForceToAtomRow()

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

virtual

Implements OpenMD::ForceDecomposition.

Definition at line 974 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 1336 of file ForceMatrixDecomposition.cpp.

◆ collectData()

void OpenMD::ForceMatrixDecomposition::collectData ( )

virtual

Implements OpenMD::ForceDecomposition.

Definition at line 579 of file ForceMatrixDecomposition.cpp.

◆ collectIntermediateData()

void OpenMD::ForceMatrixDecomposition::collectIntermediateData ( )

virtual

Implements OpenMD::ForceDecomposition.

Definition at line 523 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 786 of file ForceMatrixDecomposition.cpp.

References collectSelfData().

Referenced by collectSelfData().

◆ distributeData()

void OpenMD::ForceMatrixDecomposition::distributeData ( )

virtual

Implements OpenMD::ForceDecomposition.

Definition at line 459 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 114 of file ForceMatrixDecomposition.cpp.

References distributeInitialData(), OpenMD::PairList::hasPair(), and OpenMD::ForceDecomposition::toposForAtom.

Referenced by distributeInitialData().

◆ distributeIntermediateData()

void OpenMD::ForceMatrixDecomposition::distributeIntermediateData ( )

virtual

Implements OpenMD::ForceDecomposition.

Definition at line 558 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 962 of file ForceMatrixDecomposition.cpp.

References excludeAtomPair().

Referenced by excludeAtomPair().