This class describes a dynamical particle system. More...

Constructors and destructors
	SBMDynamicalModelParticleSystem ()
	Builds an empty particle system

	SBMDynamicalModelParticleSystem (const SBNodeIndexer &nodeIndexer)
	Builds a particle system associated to a set of nodes.

virtual	~SBMDynamicalModelParticleSystem ()
	Deletes the particle system.

Identity
virtual SBDDataGraphNode::Type	getType () const override
	Returns the type of the data graph node (returns SBDDataGraphNode::DynamicalModelParticleSystem)

virtual SBDDataGraphNode::Type	getDynamicalModelType () const override
	Returns the dynamical model type (returns SBDDataGraphNode::DynamicalModelParticleSystem)

Simulation
virtual void	updateStructuralNodes () override
	Updates the structural nodes based on the state of the particle system.

virtual bool	enforcePeriodicBoundaryConditions () override
	Enforces the periodic boundary conditions.

int	roundForPBC (const SBQuantity::length &d)

void	correctDistanceWithPBC (SBLength3 &distance)

Atoms
SBPointerIndexer< SBAtom > const *	getAtomIndexer () const
	Returns the atoms associated to the particle system.

unsigned int	addAtom (SBAtom *atom)
	Adds an atom to the particle system.

void	addAtoms (const SBNodeIndexer &nodeIndexer)
	Adds atoms of a node indexer.

void	removeAtom (SBAtom *atom)
	Removes an atom from the particle system.

void	removeAtom (unsigned int atomIndex)
	Removes an atom from the particle system.

void	removeAtoms (const SBNodeIndexer &nodeIndexer)
	Removes atoms of a node indexer.

bool	getActivityFlag (SBAtom *atom) const
	Returns the activity flag of an atom.

bool	getActivityFlag (unsigned int atomIndex) const
	Returns the activity flag of an atom.

void	setActivityFlag (SBAtom *atom, bool flag)
	Sets the activity flag of an atom.

void	setActivityFlag (unsigned int atomIndex, bool flag)
	Sets the activity flag of an atom.

SBQuantity::mass	getMass (SBAtom *atom) const
	Returns the mass of an atom.

SBQuantity::mass	getMass (unsigned int atomIndex) const
	Returns the mass of an atom.

void	setMass (SBAtom *atom, SBQuantity::mass mass)
	Sets the mass of an atom.

void	setMass (unsigned int atomIndex, SBQuantity::mass mass)
	Sets the mass of an atom.

SBQuantity::inverseMass	getInverseMass (SBAtom *atom) const
	Returns the inverse mass of an atom.

SBQuantity::inverseMass	getInverseMass (unsigned int atomIndex) const
	Returns the inverse mass of an atom.

Position buffer
virtual SBPosition3 const &	getPosition (unsigned int i) const
	Returns the position of an atom.

virtual unsigned int	getNumberOfChangedPositions () const override
	Returns the number of changed positions.

virtual unsigned int	getChangedPositionIndex (unsigned int i) const override
	Returns the index of an changed position.

virtual bool	getPositionChanged (unsigned int i) const override
	Returns whether position `i` has been changed since the last flush.

virtual void	setPosition (unsigned int i, const SBPosition3 &newPosition)
	Updates the position of an atom.

virtual void	flushPositionBuffer () override
	Flushes the position buffer.

Momentum buffer
virtual SBMomentum3 const &	getMomentum (unsigned int i) const
	Returns the momentum of an atom.

virtual unsigned int	getNumberOfChangedMomentums () const
	Returns the number of changed momentums.

virtual unsigned int	getChangedMomentumIndex (unsigned int i) const
	Returns the index of an changed momentum.

virtual void	setMomentum (unsigned int i, const SBMomentum3 &newMomentum)
	Updates the momentum of an atom.

virtual void	flushMomentumBuffer ()
	Flushes the momentum buffer.

Debugging
virtual void	print (unsigned int offset=0) const override
	Prints debugging information.

	SB_DECLARE_DATA (SBMDynamicalModelParticleSystem)

Additional Inherited Members
Public Types inherited from SBDDataGraphNode
enum	Type { Undefined , StructuralModel , StructuralModelNode , StructuralModelConformation , Conformation , StructuralModelPath , Path , StructuralModelNodeGroup , StructuralGroup , StructuralModelNodeRoot , Root , StructuralModelNodeAtom , Atom , StructuralModelNodeBond , Bond , StructuralModelNodeHydrogenBond , HydrogenBond , StructuralModelNodeHydrogenBondGroup , HydrogenBondGroup , StructuralModelNodeResidue , Residue , StructuralModelNodeSegment , Segment , StructuralModelNodeChain , Chain , StructuralModelNodeMolecule , Molecule , StructuralModelNodeBackbone , Backbone , StructuralModelNodeSideChain , SideChain , VisualModel , VisualModelMesh , Mesh , DynamicalModel , DynamicalModelParticleSystem , ParticleSystem , DynamicalModelRigidBodySystem , RigidBodySystem , DynamicalModelArticulatedBodySystem , ArticulatedBodySystem , DynamicalModelNode , DynamicalNode , DynamicalModelNodeGroup , DynamicalGroup , DynamicalModelNodeRoot , DynamicalRoot , DynamicalModelNodeParticle , Particle , DynamicalModelNodeRigidBody , RigidBody , DynamicalModelNodeArticulatedBody , ArticulatedBody , InteractionModel , InteractionModelParticleSystem , InteractionModelRigidBodySystem , InteractionModelArticulatedBodySystem , PropertyModel , PropertyModelFunction , Simulator , SimulatorParticleSystem , SimulatorRigidBodySystem , SimulatorArticulatedBodySystem , StateUpdater , StateUpdaterParticleSystem , StateUpdaterRigidBodySystem , StateUpdaterArticulatedBodySystem , Animation , Camera , Document , DocumentManager , File , Folder , Label , Light , Note , Presentation , RenderPreset , DataGraphNodeGroup , NodeGroup , Controller , ControllerNode , Asset }
	The type of the data graph node. More...

enum class	RenderingPass { Setup , OpaqueGeometry , SelectableGeometry , ShadowingGeometry , TransparentGeometry , Interface , Text }
	The rendering pass. More...

Public Member Functions inherited from SBMDynamicalModel
virtual bool	isSerializable () const override
	Returns true when the class is serializable.

virtual void	serialize (SBCSerializer *serializer, const SBNodeIndexer &nodeIndexer, const SBVersionNumber &sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber &classVersionNumber=SBVersionNumber(1, 0, 0)) const override
	Serializes the node.

virtual void	unserialize (SBCSerializer *serializer, const SBNodeIndexer &nodeIndexer, const SBVersionNumber &sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber &classVersionNumber=SBVersionNumber(1, 0, 0)) override
	Unserializes the node.

SBMDynamicalModelNodeRoot *	getDynamicalRoot () const
	Returns the root of the dynamical model.

virtual SBMDynamicalModel *	clone () override
	Returns a copy of the node and its descendants.

virtual SBDDataGraphNode::Type	getModelType () const override
	Returns the model type.

SBIAPosition3 const &	getPeriodicBoundaryConditions () const
	Returns the periodic boundary conditions.

void	setPeriodicBoundaryConditions (SBIAPosition3 const &box)
	Sets the periodic boundary conditions.

bool	getPeriodicBoundaryConditionsFlag () const
	Returns the periodic boundary conditions flag.

void	setPeriodicBoundaryConditionsFlag (bool flag)
	Sets the periodic boundary conditions flag.

void	connectDynamicalSignalToSlot (SBCReferenceTarget referenceTarget, void(SBCReferenceTarget::functionPointer)(SBDynamicalEvent ), SBCReferenceTarget nextReferenceTarget=0, void(SBCReferenceTarget::nextFunctionPointer)(SBDynamicalEvent )=0)
	Connects the dynamical signal to a slot.

bool	dynamicalSignalIsConnectedToSlot (SBCReferenceTarget referenceTarget, void(SBCReferenceTarget::functionPointer)(SBDynamicalEvent *)) const
	Returns true if and only if the dynamical signal is connected to a given slot.

void	disconnectDynamicalSignalFromSlot (SBCReferenceTarget referenceTarget, void(SBCReferenceTarget::functionPointer)(SBDynamicalEvent *))
	Disconnects the dynamical signal from a slot.

virtual void	getNodes (SBNodeIndexer &nodeIndexer, SBNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const override
	Collects nodes into `nodeIndexer`, based on a `nodeType`, a selection status and a `visitPredicate`, with or without dependencies.

virtual void	getNodes (SBNodeIndexer &nodeIndexer, const SBNodePredicate &selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const override
	Collects nodes into `nodeIndexer`, based on a `selectionPredicate` and a `visitPredicate`, with or without dependencies.

virtual bool	hasNode (SBNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const override
	Checks for nodes based on a `nodeType`, a selection status and a `visitPredicate`, with or without dependencies.

virtual bool	hasNode (const SBNodePredicate &selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const override
	Checks for nodes based on a `selectionPredicate` and a `visitPredicate`, with or without dependencies.

virtual void	forEachNodeDepthFirst (void(action)(SBDDataGraphNode node)) override
	Performs an action on each node.

virtual void	forEachNodeDepthFirst (SBCClass object, void(SBCClass::action)(SBDDataGraphNode *node)) override
	Performs an action on each node.

	SB_DECLARE_DATA (SBMDynamicalModel)

Public Member Functions inherited from SBMModel
virtual	~SBMModel ()
	Delete the model.

SBMModel *	getNextModel () const
	Returns the next model in the parent.

SBMModel *	getPreviousModel () const
	Returns the previous model in the parent.

virtual unsigned int	getOpacity () const override
	Returns the opacity.

virtual void	setOpacity (unsigned int opacity) override
	Sets the opacity.

virtual unsigned int	getMinimumOpacity () const override
	Returns the minimum opacity.

virtual unsigned int	getTransparency () const override
	Returns the transparency.

virtual void	setTransparency (unsigned int transparency) override
	Sets the transparency.

virtual unsigned int	getMaximumTransparency () const override
	Returns the maximum transparency.

bool	getShadowingFlag () const
	Returns whether the model casts shadows.

void	setShadowingFlag (bool shadowingFlag)
	Sets whether the model casts shadows.

	SB_NODE_GETTER_0 (, SBDDataGraphNode::Type, GetModelType)

	SB_NODE_PREDICATE_1 (, IsModelType, SBDDataGraphNode::Type)

	SB_DECLARE_DATA (SBMModel)

Public Member Functions inherited from SBDDataGraphNode
SBDDataGraphNode *	getParent () const
	Returns the parent of the node.

SBDDataGraphNode *	getThisNode () const
	Returns the pointer to this node.

SBDDataGraphNode *	getNextNode () const
	Returns the pointer to the next node in the children of the node's parent.

SBDDataGraphNode *	getPreviousNode () const
	Returns the pointer to the previous node in the children of the node's parent.

SBDDataGraphNode *	getNextNode (SBDDataGraphNode::Type nodeType) const
	Returns the pointer to the next node with type `nodeType` in the children of the node's parent.

SBDDataGraphNode *	getPreviousNode (SBDDataGraphNode::Type nodeType) const
	Returns the pointer to the previous node with type `nodeType` in the children of the node's parent.

SBDDocument *	getDocument () const
	Returns the document the node belongs to.

virtual bool	canAddChild (const SBDDataGraphNode node, const SBDDataGraphNode nextNode=nullptr) const
	Returns whether this node can add `node` as a child.

virtual bool	canAddChildType (SBDDataGraphNode::Type nodeType) const
	Returns whether this node can add a node with type `nodeType` as a child.

virtual bool	canHaveDescendantType (SBDDataGraphNode::Type nodeType) const
	Returns whether this node can have a node with type `nodeType` as a descendant.

virtual bool	addChild (SBDDataGraphNode node, SBDDataGraphNode nextNode=nullptr)
	Adds a child to the node.

virtual bool	removeChild (SBDDataGraphNode *node)
	Removes a child from the node.

bool	hasOneOf (const SBNodeIndexer &nodeIndexer) const
	Returns true if and only if this node is one of the nodes of the `nodeIndexer`, or is the ancestor of one of them, or is a group that stores one of them.

bool	descendsFrom (const SBDDataGraphNode *node) const
	Returns true if and only if this node is `node`, or descends from it.

bool	descendsFrom (const SBNodeIndexer &nodeIndexer) const
	Returns true if and only if this node is one of the nodes of the `nodeIndexer`, or descends from one of them.

bool	descendsFrom (SBPointerIndexer< SBDDataGraphNode > *nodePointerIndexer) const
	Returns true if and only if this node is one of the nodes of the `nodePointerIndexer`, or descends from one of them.

bool	isIn (const SBDDataGraphNode *node) const
	Returns true if and only if this node is `node`, or descends from it, or belongs to a group stored in `node`.

bool	isIn (const SBNodeIndexer &nodeIndexer) const
	Returns true if and only if this node is one of the nodes of the `nodeIndexer`, or descends from one of them, or belongs to a group stored in one of the nodes of the `nodeIndexer`.

bool	isIn (SBPointerIndexer< SBDDataGraphNode > *nodePointerIndexer) const
	Returns true if and only if this node is one of the nodes of the `nodePointerIndexer`, or descends from one of them, or belongs to a group stored in of the nodes of the `nodePointerIndexer`.

bool	isOneOf (const SBNodeIndexer &nodeIndexer) const
	Returns true if and only if this node is one of the nodes of the `nodeIndexer`.

bool	isOneOf (SBPointerIndexer< SBDDataGraphNode > *nodePointerIndexer) const
	Returns true if and only if this node is one of the nodes of the `nodePointerIndexer`.

SBDDataGraphNode *	getRoot () const
	Returns the root of the hierarchy the node belongs to.

unsigned int	getNodeIndex () const
	Returns the node index (unique in the whole data graph, but non-persistent)

std::string	getTypeString (bool humanReadable=false) const
	Returns a string describing the type of the data graph node.

virtual std::string const &	getName () const
	Returns the name of the node.

virtual void	setName (const std::string &name)
	Sets the name of the node.

bool	isType (Type type) const
	Returns true when the type of the node corresponds to `type`.

bool	isModel () const
	Returns true when the node is a model.

bool	isAtom () const
	Returns true when the node is an atom.

bool	isBond () const
	Returns true when the node is a bond.

bool	isStructuralNode () const
	Returns true when the node is a structural node.

bool	isStructuralModel () const
	Returns true when the node is a structural model.

bool	isVisualModel () const
	Returns true when the node is a visual model.

bool	isDynamicalModel () const
	Returns true when the node is a dynamical model.

bool	isInteractionModel () const
	Returns true when the node is a interaction model.

bool	isPropertyModel () const
	Returns true when the node is a property model.

bool	isMesh () const
	Returns true when the node is a mesh.

bool	isLight () const
	Returns true when the node is a light.

bool	isSimulator () const
	Returns true when the node is a simulator.

bool	isBallAndStick () const
	Returns true when the node is the default ball-and-stick visual model.

bool	isLicorice () const
	Returns true when the node is the default licorice visual model.

bool	isVanDerWaals () const
	Returns true when the node is the default van der Waals visual model.

bool	isCartoon () const
	Returns true when the node is the default cartoon visual model.

bool	isRibbon () const
	Returns true when the node is the default ribbon visual model.

bool	isTube () const
	Returns true when the node is the default tube visual model.

bool	isGaussianSurface () const
	Returns true when the node is the default Gaussian surface visual model.

bool	isSolventAccessibleSurface () const
	Returns true when the node is the default solvent accessible surface visual model.

bool	isSolventExcludedSurface () const
	Returns true when the node is the default solvent excluded surface visual model.

virtual bool	isLocked () const
	Returns whether the node is locked.

virtual bool	getLockedFlag () const
	Returns the locked flag.

virtual void	setLockedFlag (bool flag)
	Sets the locked flag.

bool	isCreated () const
	Returns true if and only if the node is created.

void	create ()
	Creates the node.

bool	isErased () const
	Returns true if and only if the node is erased.

void	erase ()
	Erases the node.

virtual unsigned int	getFlags () const
	Returns the flags.

virtual unsigned int	getInheritedFlags () const
	Returns the inherited flags.

bool	isSelected () const
	Returns whether the node is selected.

bool	getSelected () const
	Returns whether the node is selected.

bool	getSelectionFlag () const
	Returns the selection flag.

void	setSelectionFlag (bool flag)
	Sets the selection flag.

bool	isVisible () const
	Returns whether the node is visible.

bool	getVisible () const
	Returns whether the node is visible.

bool	getVisibilityFlag () const
	Returns the visibility flag.

void	setVisibilityFlag (bool flag)
	Sets the visibility flag.

bool	isHighlighted () const
	Returns whether the node is highlighted.

bool	getHighlightingFlag () const
	Returns the highlighting flag.

void	setHighlightingFlag (bool flag)
	Sets the highlighting flag.

virtual void	display (RenderingPass renderingPass)
	Displays the node.

virtual void	display ()
	Displays the node (deprecated)

virtual void	displayForShadow ()
	Displays the node for shadowing purposes (deprecated)

virtual void	displayForSelection ()
	Displays the node for selection purposes (deprecated)

virtual bool	hasOpacityRange () const
	Returns whether the node has the opacity range.

virtual unsigned int	getDefaultOpacity () const
	Returns the default opacity.

virtual unsigned int	getMaximumOpacity () const
	Returns the maximum opacity.

virtual unsigned int	getOpacitySingleStep () const
	Returns the opacity single step.

virtual std::string	getOpacitySuffix () const
	Returns the opacity suffix.

virtual bool	hasTransparencyRange () const
	Returns whether the node has the transparency range.

virtual unsigned int	getDefaultTransparency () const
	Returns the default transparency.

virtual unsigned int	getMinimumTransparency () const
	Returns the minimum transparency.

virtual unsigned int	getTransparencySingleStep () const
	Returns the transparency single step.

virtual std::string	getTransparencySuffix () const
	Returns the transparency suffix.

float	getInheritedOpacity () const
	Returns the cumulative opacity, when taking into account the ascendants.

float	getInheritedTransparency () const
	Returns the cumulative transparency, when taking into account the ascendants.

bool	canAddMaterial () const
	Returns whether can add a material to the node based on its type.

bool	addMaterial (SBDDataGraphNodeMaterial *material)
	Adds a material.

bool	removeMaterial ()
	Removes the material.

void	removeMaterialsFromDescendants ()
	Removes materials from all nodes that descend from this node, but it does not remove the material from the node itself.

bool	hasMaterial () const
	Returns whether the node has a material (by itself, or inherited)

bool	ownsMaterial () const
	Returns whether the node owns a material.

SBDDataGraphNodeMaterial *	getMaterial () const
	Returns the material.

SBDDataGraphNode *	getMaterialOwner () const
	Returns the node whose material is inherited.

void	connectBaseSignalToSlot (SBCReferenceTarget referenceTarget, void(SBCReferenceTarget::functionPointer)(SBBaseEvent ), SBCReferenceTarget nextReferenceTarget=0, void(SBCReferenceTarget::nextFunctionPointer)(SBBaseEvent )=0)
	Connects the base signal to a slot.

bool	baseSignalIsConnectedToSlot (SBCReferenceTarget referenceTarget, void(SBCReferenceTarget::functionPointer)(SBBaseEvent *)) const
	Returns true when the base signal is connected to a slot.

void	disconnectBaseSignalFromSlot (SBCReferenceTarget referenceTarget, void(SBCReferenceTarget::functionPointer)(SBBaseEvent *))
	Disconnects the base signal from a slot.

unsigned int	countNodes (SBDDataGraphNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const
	Counts nodes based on a `nodeType`, a selection status and a `visitPredicate`, with or without dependencies.

unsigned int	countNodes (const SBNodePredicate &selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const
	Counts nodes based on a `selectionPredicate` and a `visitPredicate`, with or without dependencies.

virtual std::string	getHierarchyString (const std::string &separator=" / ", bool includeNodeType=false) const
	Returns a string with hierarchical information on the node and its parents names.

virtual unsigned int	getNumberOfChains ()
	Returns the number of chains.

virtual unsigned int	getNumberOfMolecules ()
	Returns the number of molecules.

virtual unsigned int	getNumberOfResidues ()
	Returns the number of residues.

virtual unsigned int	getNumberOfSegments ()
	Returns the number of segments.

virtual unsigned int	getNumberOfStructuralGroups ()
	Returns the number of structural groups.

virtual unsigned int	getNumberOfStructuralModels ()
	Returns the number of structural models.

virtual unsigned int	getNumberOfAtoms ()
	Returns the number of atoms.

virtual unsigned int	getNumberOfCarbons ()
	Returns the number of carbons.

virtual unsigned int	getNumberOfHydrogens ()
	Returns the number of hydrogens.

virtual unsigned int	getNumberOfNitrogens ()
	Returns the number of nitrogens.

virtual unsigned int	getNumberOfOxygens ()
	Returns the number of oxygens.

virtual unsigned int	getNumberOfSulfurs ()
	Returns the number of sulfurs.

virtual unsigned int	getNumberOfCoarseGrainedAtoms ()
	Returns the number of coarse-grained atoms.

virtual unsigned int	getNumberOfOtherAtoms ()
	Returns the number of other atoms.

virtual int	getSumOfFormalCharges ()
	Returns the sum of formal charges.

virtual float	getSumOfPartialCharges ()
	Returns the sum of partial charges.

virtual SBQuantity::mass	getMolecularWeight ()
	Returns the molecular weight.

	SB_DECLARE_DATA (SBDDataGraphNode)

Public Member Functions inherited from SBCReferenceTarget
unsigned int	getMemoryFootprint () const

void	printReferencesToOwners () const

	SBCReferenceTarget ()

virtual	~SBCReferenceTarget ()

Static Public Member Functions inherited from SBDDataGraphNode
static void	clone (const SBNodeIndexer &sourceNodeIndexer, SBNodeIndexer &destinationNodeIndexer)
	Clones the nodes in `sourceNodeIndexer` (treated as a whole) and places the clones in `destinationNodeIndexer`.

static SBDDataGraphNode *	getNode (unsigned int nodeIndex)
	Returns the unique node corresponding to the node index `nodeIndex`.

static std::string	getTypeString (Type type, bool humanReadable=false)
	Returns a string describing the type of the data graph node.

static bool	canAddMaterial (SBDDataGraphNode::Type nodeType)
	Returns whether can add a material to a node of type `nodeType`.

static void	forEachNodeInSelection (SBNodeIndexer &nodeIndexer, void(action)(SBDDataGraphNode node))
	Performs an action for each node in a selection.

static void	forEachNodeInSelection (SBNodeIndexer &nodeIndexer, SBCClass object, void(SBCClass::action)(SBDDataGraphNode *node))
	Performs an action for each node in a selection.

Protected Member Functions inherited from SBMDynamicalModel
	SBMDynamicalModel ()
	Builds a dynamical model.

	SBMDynamicalModel (SBMDynamicalModelData *dataPointer)
	Builds a dynamical model.

virtual	~SBMDynamicalModel ()
	Deletes the dynamical model.

Protected Member Functions inherited from SBMModel
	SBMModel ()
	Builds a model.

	SBMModel (SBMModelData *dataPointer)
	Builds a model.

Protected Member Functions inherited from SBDDataGraphNode
	SBDDataGraphNode ()
	Builds a data graph node.

	SBDDataGraphNode (SBDDataGraphNodeData *dataPointer)
	Builds a data graph node.

virtual	~SBDDataGraphNode ()
	Destroys the node.

Protected Member Functions inherited from SBCReferenceTarget
void	removeAllReferenceOwners ()

	SBCReferenceTarget (SBCReferenceTargetData *dataPointer)

Protected Attributes inherited from SBCReferenceTarget
SBCReferenceTargetData *	dataPointer

Detailed Description

The class SBMDynamicalModelParticleSystem describes a particle system in SAMSON, i.e. a dynamical system composed of particles. A particle system has two buffers - a position buffer and a momentum buffer - which may be used to write adaptive simulation algorithms.

Short name: SBParticleSystem

See also: SBCContainerBuffer

Constructor & Destructor Documentation

◆ SBMDynamicalModelParticleSystem()

SBMDynamicalModelParticleSystem::SBMDynamicalModelParticleSystem ( )

The default constructor builds an empty particle system

See also: addAtom

◆ ~SBMDynamicalModelParticleSystem()

SBMDynamicalModelParticleSystem::~SBMDynamicalModelParticleSystem ( )

virtual

Deletes the model.

Member Function Documentation

◆ enforcePeriodicBoundaryConditions()

bool SBMDynamicalModelParticleSystem::enforcePeriodicBoundaryConditions ( )

overridevirtual

Reimplemented from SBMDynamicalModel.

◆ flushPositionBuffer()

void SBMDynamicalModelParticleSystem::flushPositionBuffer ( )

overridevirtual

Reimplemented from SBMDynamicalModel.

◆ getChangedMomentumIndex()

unsigned int SBMDynamicalModelParticleSystem::getChangedMomentumIndex ( unsigned int i ) const

virtual

This function returns the index of the i-th changed momentum. This may be used by adaptive simulation algorithms, ir order to know which momenta have been changed at a given time step.

Assume for example that particle 17, 32, and 529 have had their momentum changed since the last flush of the momentum buffer. Then the following code:

unsigned int nChangedMomenta=particleSystem->getNumberOfChangedMomentums();
 
for (unsigned int i=0;i<nChangedMomenta;i++) {
 
    // changedMomentumIndex is the index of the i-th changed momentum
    unsigned int changedMomentumIndex=particleSystem->getChangedMomentumIndex(i); 
    std::cout << changedMomentumIndex << std::endl;
 
}

outputs

17
32
529

Parameters

i	The index of the changed momentum.

See also: getMomentum, getChangedMomentumIndex, flushMomentumBuffer

◆ getChangedPositionIndex()

unsigned int SBMDynamicalModelParticleSystem::getChangedPositionIndex ( unsigned int i ) const

overridevirtual

Reimplemented from SBMDynamicalModel.

◆ getDynamicalModelType()

SBDDataGraphNode::Type SBMDynamicalModelParticleSystem::getDynamicalModelType ( ) const

overridevirtual

Reimplemented from SBMDynamicalModel.

◆ getNumberOfChangedMomentums()

unsigned int SBMDynamicalModelParticleSystem::getNumberOfChangedMomentums ( ) const

virtual

This function returns the number of changed momenta since the last flush of the momentum buffer.

See also: getMomentum, getChangedMomentumIndex, flushMomentumBuffer

◆ getNumberOfChangedPositions()

unsigned int SBMDynamicalModelParticleSystem::getNumberOfChangedPositions ( ) const

overridevirtual

Reimplemented from SBMDynamicalModel.

◆ getPositionChanged()

bool SBMDynamicalModelParticleSystem::getPositionChanged ( unsigned int i ) const

overridevirtual

Reimplemented from SBMDynamicalModel.

◆ getType()

SBDDataGraphNode::Type SBMDynamicalModelParticleSystem::getType ( ) const

overridevirtual

Reimplemented from SBMDynamicalModel.

◆ print()

void SBMDynamicalModelParticleSystem::print ( unsigned int offset = 0 ) const

overridevirtual

Reimplemented from SBMDynamicalModel.

◆ updateStructuralNodes()

void SBMDynamicalModelParticleSystem::updateStructuralNodes ( )

overridevirtual

Reimplemented from SBMDynamicalModel.

Constructors and destructors

Identity

Simulation

Atoms

Position buffer

Momentum buffer

Debugging

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SBMDynamicalModelParticleSystem()

◆ ~SBMDynamicalModelParticleSystem()

Member Function Documentation

◆ enforcePeriodicBoundaryConditions()

◆ flushPositionBuffer()

◆ getChangedMomentumIndex()

◆ getChangedPositionIndex()

◆ getDynamicalModelType()

◆ getNumberOfChangedMomentums()

◆ getNumberOfChangedPositions()

◆ getPositionChanged()

◆ getType()

◆ print()

◆ updateStructuralNodes()