SBMDynamicalModelParticleSystem Class Reference
This class describes a dynamical particle system. More...
Constructors and destructors | |
| SBMDynamicalModelParticleSystem () | |
| Builds an empty particle system. More... | |
| SBMDynamicalModelParticleSystem (const SBNodeIndexer &nodeIndexer) | |
| Builds a particle system associated to a set of nodes. | |
| virtual | ~SBMDynamicalModelParticleSystem () |
| Deletes the particle system. More... | |
Identity | |
| virtual SBDDataGraphNode::Type | getType () const |
| Returns the type of the data graph node (returns SBDDataGraphNode::DynamicalModelParticleSystem) | |
| virtual SBDDataGraphNode::Type | getDynamicalModelType () const |
| Returns the dynamical model type (returns SBDDataGraphNode::DynamicalModelParticleSystem) | |
Simulation | |
| virtual void | updateStructuralNodes () |
| Updates the structural nodes based on the state of the particle system. | |
| virtual bool | enforcePeriodicBoundaryConditions () |
| Enforces the periodic boundary conditions. | |
| int | roundForPBC (const SBQuantity::position &d) |
| void | correctDistanceWithPBC (SBLength3 &distance) |
Particles | |
| SBPointerIndexer< SBStructuralParticle > const * | getStructuralParticleIndexer () const |
| Returns the particle index of the particle system. | |
| unsigned int | addParticle (SBStructuralParticle *particle) |
| Adds a particle to the particle system. | |
| void | addParticles (const SBNodeIndexer &nodeIndexer) |
| Adds particles from a node indexer. | |
| void | removeParticle (SBStructuralParticle *particle) |
| Removes a particle from the particle system. | |
| void | removeParticle (unsigned int particleIndex) |
| Removes a particle from the particle system. | |
| void | removeParticles (const SBNodeIndexer &nodeIndexer) |
| Removes particles from a node indexer. | |
| bool | getActivityFlag (SBStructuralParticle *particle) const |
| Returns the activity flag of a particle. | |
| bool | getActivityFlag (unsigned int particleIndex) const |
| Returns the activity flag of a particle. | |
| void | setActivityFlag (SBStructuralParticle *particle, bool flag) |
| Sets the activity flag of a particle. | |
| void | setActivityFlag (unsigned int particleIndex, bool flag) |
| Sets the activity flag of a particle. | |
| SBQuantity::mass | getMass (SBStructuralParticle *particle) const |
| Returns the mass of a particle. | |
| SBQuantity::mass | getMass (unsigned int particleIndex) const |
| Returns the mass of a particle. | |
| void | setMass (SBStructuralParticle *particle, SBQuantity::mass mass) |
| Sets the mass of a particle. | |
| void | setMass (unsigned int particleIndex, SBQuantity::mass mass) |
| Sets the mass of a particle. | |
| SBQuantity::inverseMass | getInverseMass (SBStructuralParticle *particle) const |
| Returns the inverse mass of a particle. | |
| SBQuantity::inverseMass | getInverseMass (unsigned int particleIndex) const |
| Returns the inverse mass of a particle. | |
Position buffer | |
| virtual SBPosition3 const & | getPosition (unsigned int i) const |
| Returns the position of a particle. | |
| virtual unsigned int | getNumberOfChangedPositions () const |
| Returns the number of changed positions. | |
| virtual unsigned int | getChangedPositionIndex (unsigned int i) const |
| Returns the index of an changed position. | |
| virtual bool | getPositionChanged (unsigned int i) const |
Returns whether position i has been changed since the last flush. | |
| virtual void | setPosition (unsigned int i, const SBPosition3 &newPosition) |
| Updates the position of a particle. | |
| virtual void | flushPositionBuffer () |
| Flushes the position buffer. | |
Momentum buffer | |
| virtual SBMomentum3 const & | getMomentum (unsigned int i) const |
| Returns the momentum of a particle. | |
| virtual unsigned int | getNumberOfChangedMomentums () const |
| Returns the number of changed momentums. More... | |
| virtual unsigned int | getChangedMomentumIndex (unsigned int i) const |
| Returns the index of an changed momentum. More... | |
| virtual void | setMomentum (unsigned int i, const SBMomentum3 &newMomentum) |
| Updates the momentum of a particle. | |
| virtual void | flushMomentumBuffer () |
| Flushes the momentum buffer. | |
Debugging | |
| virtual void | print (unsigned int offset=0) const |
| Prints debugging information. | |
Additional Inherited Members | |
 Public Types inherited from SBDDataGraphNode | |
| enum | Type { Undefined, StructuralModel, StructuralModelNode, StructuralModelConformation, Conformation, StructuralModelPath, Path, StructuralModelNodeGroup, StructuralGroup, StructuralModelNodeRoot, Root, StructuralModelNodeParticle, StructuralParticle, StructuralModelNodeAtom, Atom, StructuralModelNodePseudoAtom, PseudoAtom, StructuralModelNodeBond, Bond, StructuralModelNodeResidue, Residue, StructuralModelNodeSegment, Segment, StructuralModelNodeProtein, Protein, StructuralModelNodeChain, Chain, StructuralModelNodeMolecule, Molecule, StructuralModelNodeBackbone, Backbone, StructuralModelNodeSideChain, SideChain, VisualModel, DynamicalModel, DynamicalModelParticleSystem, ParticleSystem, DynamicalModelRigidBodySystem, RigidBodySystem, DynamicalModelArticulatedBodySystem, ArticulatedBodySystem, DynamicalModelNode, DynamicalNode, DynamicalModelNodeGroup, DynamicalGroup, DynamicalModelNodeRoot, DynamicalRoot, DynamicalModelNodeParticle, DynamicalParticle, DynamicalModelNodeRigidBody, RigidBody, DynamicalModelNodeArticulatedBody, ArticulatedBody, InteractionModel, InteractionModelParticleSystem, InteractionModelRigidBodySystem, InteractionModelArticulatedBodySystem, PropertyModel, PropertyModelFunction, Simulator, SimulatorParticleSystem, SimulatorRigidBodySystem, SimulatorArticulatedBodySystem, StateUpdater, StateUpdaterParticleSystem, StateUpdaterRigidBodySystem, StateUpdaterArticulatedBodySystem, DocumentManager, Document, Folder, Camera, Label, DataGraphNodeGroup, NodeGroup, Controller, ControllerNode } |
| The type of the data graph node. More... | |
| Public Member Functions inherited from SBMDynamicalModel | |
| bool | isSerializable () const |
| 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 |
| 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)) |
| Unserializes the node. | |
| SBMDynamicalModelNodeRoot * | getDynamicalRoot () const |
| Returns the root of the dynamical model. | |
| virtual SBMDynamicalModel * | clone () |
| Returns a copy of the node and its descendants. | |
| virtual SBDDataGraphNode::Type | getModelType () const |
| 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, const SBNodePredicate &selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) |
| Returns some nodes. | |
| virtual void | forEachNodeDepthFirst (void(*action)(SBDDataGraphNode *node)) |
| Performs an action on each node. | |
| virtual void | forEachNodeDepthFirst (SBCClass *object, void(SBCClass::*action)(SBDDataGraphNode *node)) |
| Performs an action on each node. | |
| Public Member Functions inherited from SBMModel | |
| virtual | ~SBMModel () |
| Delete the model. | |
| bool | isSerializable () const |
| Returns true. | |
| SBMModel * | getNextModel () const |
| Returns the next model in the parent. | |
| SBMModel * | getPreviousModel () const |
| Returns the previous model in the parent. | |
| std::string const & | getName () const |
| Returns the name of the model. | |
| void | setName (const std::string &name) |
| Sets the name of the model. | |
| Public Member Functions inherited from SBDDataGraphNode | |
| SBDDataGraphNode * | getParent () const |
| Returns the parent of the node. More... | |
| SBDDataGraphNode * | getThisNode () const |
| Returns the pointer to this node. More... | |
| SBDDataGraphNode * | getNextNode () const |
| Returns the pointer to the next node in the children of the node's parent. More... | |
| SBDDataGraphNode * | getPreviousNode () const |
| Returns the pointer to the previous node in the children of the node's parent. More... | |
| SBDDataGraphNode * | getNextNode (SBDDataGraphNode::Type nodeType) const |
Returns the pointer to the next node with type nodeType in the children of the node's parent. More... | |
| SBDDataGraphNode * | getPreviousNode (SBDDataGraphNode::Type nodeType) const |
Returns the pointer to the previous node with type nodeType in the children of the node's parent. More... | |
| SBDDocument * | getDocument () const |
| Returns the document the node belongs to. More... | |
| virtual bool | canAddChild (SBDDataGraphNode *node, SBDDataGraphNode *nextNode=0) const |
Returns whether this node can add node as a child. More... | |
| virtual bool | canAddChildType (SBDDataGraphNode::Type nodeType) const |
Returns whether this node can add a node with type nodeType as a child. More... | |
| virtual bool | addChild (SBDDataGraphNode *node, SBDDataGraphNode *nextNode=0) |
| Adds a child to the node. More... | |
| virtual bool | removeChild (SBDDataGraphNode *node) |
| Removes a child from the node. More... | |
| 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. More... | |
| bool | isIn (SBDDataGraphNode *node) const |
Returns true if and only if this node is node, or descends from it. More... | |
| 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. More... | |
| 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. More... | |
| bool | isOneOf (const SBNodeIndexer &nodeIndexer) const |
Returns true if and only if this node is one of the nodes of the nodeIndexer. More... | |
| bool | isOneOf (SBPointerIndexer< SBDDataGraphNode > *nodePointerIndexer) const |
Returns true if and only if this node is one of the nodes of the nodePointerIndexer. More... | |
| SBDDataGraphNode * | getRoot () const |
| Returns the root of the hierarchy the node belongs to. More... | |
| unsigned int | getNodeIndex () const |
| Returns the node index (unique in the whole data graph, but non-persistent) More... | |
| 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 | 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 | isSimulator () const |
| Returns true when the node is a simulator. | |
| bool | isStructuralParticle () const |
| Returns true when the node is a structural particle (an atom or a pseudo-atom) | |
| bool | isCreated () const |
| Returns true if and only if the node is created. More... | |
| void | create () |
| Creates the node. More... | |
| bool | isErased () const |
| Returns true if and only if the node is erased. More... | |
| void | erase () |
| Erases the node. More... | |
| unsigned int | getFlags () const |
| Returns the flags. More... | |
| unsigned int | getInheritedFlags () const |
| Returns the inherited flags. More... | |
| bool | isSelected () const |
| Returns whether the node is selected. More... | |
| bool | getSelected () const |
| Returns whether the node is visible. | |
| bool | getSelectionFlag () const |
| Returns the selection flag. More... | |
| void | setSelectionFlag (bool flag) |
| Sets the selection flag. More... | |
| bool | isVisible () const |
| Returns whether the node is visible. More... | |
| bool | getVisible () const |
| Returns whether the node is visible. | |
| bool | getVisibilityFlag () const |
| Returns the visibility flag. More... | |
| void | setVisibilityFlag (bool flag) |
| Sets the visibility flag. More... | |
| bool | isHighlighted () const |
| Returns whether the node is highlighted. More... | |
| bool | getHighlightingFlag () const |
| Returns the highlighting flag. More... | |
| void | setHighlightingFlag (bool flag) |
| Sets the highlighting flag. More... | |
| void | connectBaseSignalToSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBBaseEvent *), SBCReferenceTarget *nextReferenceTarget=0, void(SBCReferenceTarget::*nextFunctionPointer)(SBBaseEvent *)=0) |
| Connects the base signal to a slot. More... | |
| 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 (const SBNodePredicate &selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) |
Collects nodes into nodeIndexer, based on a selectionPredicate and a visitPredicate, with our without dependencies. More... | |
| bool | addMaterial (SBDDataGraphNodeMaterial *material) |
| Adds a material. More... | |
| bool | removeMaterial () |
| Removes the material. More... | |
| SBDDataGraphNodeMaterial * | getMaterial () const |
| Returns the material. More... | |
| SBDDataGraphNode * | getMaterialOwner () const |
| Returns the node whose material is inherited. More... | |
| Public Member Functions inherited from SBCReferenceTarget | |
| SBCReferenceTarget () | |
| virtual | ~SBCReferenceTarget () |
| unsigned int | getMemoryFootprint () const |
| void | printReferencesToOwners () const |
| Static Public Member Functions inherited from SBDDataGraphNode | |
| static SBDDataGraphNode * | getNode (unsigned int nodeIndex) |
Returns the unique node corresponding to the node index nodeIndex. More... | |
| static std::string | getTypeString (Type type) |
| Returns a string describing the type of the data graph node. More... | |
| 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. More... | |
| SBDDataGraphNode (SBDDataGraphNodeData *dataPointer) | |
| Builds a data graph node. | |
| virtual | ~SBDDataGraphNode () |
| Destroys the node. More... | |
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
- addParticle
◆ ~SBMDynamicalModelParticleSystem()
|
virtual |
Deletes the model.
Member Function Documentation
◆ getChangedMomentumIndex()
|
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.
◆ getNumberOfChangedMomentums()
|
virtual |
This function returns the number of changed momenta since the last flush of the momentum buffer.