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molecule Class Reference

Foam::molecule. More...

Inheritance diagram for molecule:
Collaboration diagram for molecule:

Classes

class  constantProperties
 Class to hold molecule constant properties. More...
 
class  iNew
 Factory class to read-construct particles used for. More...
 
class  trackingData
 Class used to pass tracking data to the trackToFace function. More...
 

Public Types

enum  specialTypes { SPECIAL_TETHERED = -1, SPECIAL_FROZEN = -2, NOT_SPECIAL = 0, SPECIAL_USER = 1 }
 

Public Member Functions

 molecule (const polyMesh &mesh, const barycentric &coordinates, const label celli, const label tetFacei, const label tetPti, const tensor &Q, const vector &v, const vector &a, const vector &pi, const vector &tau, const vector &specialPosition, const constantProperties &constProps, const label special, const label id)
 Construct from components. More...
 
 molecule (const polyMesh &mesh, const vector &position, const label celli, const tensor &Q, const vector &v, const vector &a, const vector &pi, const vector &tau, const vector &specialPosition, const constantProperties &constProps, const label special, const label id)
 Construct from a position and a cell, searching for the rest of the. More...
 
 molecule (const polyMesh &mesh, Istream &is, bool readFields=true)
 Construct from Istream. More...
 
autoPtr< particleclone () const
 Construct and return a clone. More...
 
bool move (moleculeCloud &, trackingData &, const scalar trackTime)
 
virtual void transformProperties (const transformer &)
 Transform the physical properties of the particle. More...
 
void setSitePositions (const constantProperties &constProps)
 
void setSiteSizes (label size)
 
const tensorQ () const
 
tensorQ ()
 
const vectorv () const
 
vectorv ()
 
const vectora () const
 
vectora ()
 
const vectorpi () const
 
vectorpi ()
 
const vectortau () const
 
vectortau ()
 
const List< vector > & siteForces () const
 
List< vector > & siteForces ()
 
const List< vector > & sitePositions () const
 
List< vector > & sitePositions ()
 
const vectorspecialPosition () const
 
vectorspecialPosition ()
 
scalar potentialEnergy () const
 
scalar & potentialEnergy ()
 
const tensorrf () const
 
tensorrf ()
 
label special () const
 
bool tethered () const
 
label id () const
 
bool hitPatch (moleculeCloud &cloud, trackingData &td)
 Overridable function to handle the particle hitting a patch. More...
 
void hitProcessorPatch (moleculeCloud &cloud, trackingData &td)
 Overridable function to handle the particle hitting a processorPatch. More...
 
void hitWallPatch (moleculeCloud &cloud, trackingData &td)
 Overridable function to handle the particle hitting a wallPatch. More...
 
- Public Member Functions inherited from particle< Type >
 TypeName ("particle")
 Runtime type information. More...
 
 particle (const polyMesh &mesh, const barycentric &coordinates, const label celli, const label tetFacei, const label tetPti)
 Construct from components. More...
 
 particle (const polyMesh &mesh, const vector &position, const label celli)
 Construct from a position and a cell, searching for the rest of the. More...
 
 particle (const polyMesh &mesh, Istream &, bool readFields=true)
 Construct from Istream. More...
 
 particle (const particle &p)
 Construct as a copy. More...
 
 particle (const particle &p, const polyMesh &mesh)
 Construct as a copy with references to a new mesh. More...
 
virtual ~particle ()
 Destructor. More...
 
label getNewParticleID () const
 Get unique particle creation id. More...
 
const polyMeshmesh () const
 Return the mesh database. More...
 
const barycentriccoordinates () const
 Return current particle coordinates. More...
 
label cell () const
 Return current cell particle is in. More...
 
label tetFace () const
 Return current tet face particle is in. More...
 
label tetPt () const
 Return current tet face particle is in. More...
 
label face () const
 Return current face particle is on otherwise -1. More...
 
scalar stepFraction () const
 Return the fraction of time-step completed. More...
 
scalar & stepFraction ()
 Return the fraction of time-step completed. More...
 
label origProc () const
 Return the originating processor ID. More...
 
labelorigProc ()
 Return the originating processor ID. More...
 
label origId () const
 Return the particle ID on the originating processor. More...
 
labelorigId ()
 Return the particle ID on the originating processor. More...
 
Pair< scalar > stepFractionSpan () const
 Return the step fraction change within the overall time-step. More...
 
scalar currentTimeFraction () const
 Return the current fraction within the timestep. This differs. More...
 
tetIndices currentTetIndices () const
 Return the indices of the current tet that the. More...
 
barycentricTensor currentTetTransform () const
 Return the current tet transformation tensor. More...
 
vector normal () const
 Return the normal of the tri on tetFacei_ for the. More...
 
bool onFace () const
 Is the particle on a face? More...
 
bool onInternalFace () const
 Is the particle on an internal face? More...
 
bool onBoundaryFace () const
 Is the particle on a boundary face? More...
 
label patch () const
 Return the index of patch that the particle is on. More...
 
vector position () const
 Return current particle position. More...
 
void reset ()
 Set step fraction and behind data to zero in preparation for a new. More...
 
scalar track (const vector &displacement, const scalar fraction)
 Track along the displacement for a given fraction of the overall. More...
 
scalar trackToCell (const vector &displacement, const scalar fraction)
 As particle::track, but stops when a new cell is reached. More...
 
scalar trackToFace (const vector &displacement, const scalar fraction)
 As particle::track, but stops when a face is hit. More...
 
scalar trackToTri (const vector &displacement, const scalar fraction, label &tetTriI)
 As particle::trackToFace, but stops when a tet triangle is hit. On. More...
 
scalar trackToStationaryTri (const vector &displacement, const scalar fraction, label &tetTriI)
 As particle::trackToTri, but for stationary meshes. More...
 
scalar trackToMovingTri (const vector &displacement, const scalar fraction, label &tetTriI)
 As particle::trackToTri, but for moving meshes. More...
 
template<class TrackCloudType >
void hitFace (const vector &displacement, const scalar fraction, TrackCloudType &cloud, trackingData &td)
 Hit the current face. If the current face is internal than this. More...
 
template<class TrackCloudType >
void hitFaceNoChangeToMasterPatch (const vector &displacement, const scalar fraction, TrackCloudType &cloud, trackingData &td)
 As above, but does not change the master patch. Needed in order for. More...
 
template<class TrackCloudType >
scalar trackToAndHitFace (const vector &displacement, const scalar fraction, TrackCloudType &cloud, trackingData &td)
 Convenience function. Combines trackToFace and hitFace. More...
 
vector deviationFromMeshCentre () const
 Get the displacement from the mesh centre. Used to correct the. More...
 
void patchData (vector &normal, vector &displacement) const
 Get the normal and displacement of the current patch location. More...
 
void prepareForParallelTransfer ()
 Convert global addressing to the processor patch local equivalents. More...
 
void correctAfterParallelTransfer (const label patchi, trackingData &td)
 Convert processor patch addressing to the global equivalents. More...
 
void prepareForInteractionListReferral (const transformer &transform)
 Break the topology and store the particle position so that the. More...
 
void correctAfterInteractionListReferral (const label celli)
 Correct the topology after referral. The particle may still be. More...
 
label procTetPt (const polyMesh &procMesh, const label procCell, const label procTetFace) const
 Return the tet point appropriate for decomposition or reconstruction. More...
 
void autoMap (const vector &position, const mapPolyMesh &mapper)
 Map after a topology change. More...
 
void writePosition (Ostream &) const
 Write the particle position and cell. More...
 
template<class TrackCloudType >
Foam::scalar trackToAndHitFace (const vector &displacement, const scalar fraction, TrackCloudType &cloud, trackingData &td)
 

Static Public Member Functions

static void readFields (Cloud< molecule > &mC)
 
static void writeFields (const Cloud< molecule > &mC)
 
- Static Public Member Functions inherited from particle< Type >
static string propertyList ()
 
template<class TrackCloudType >
static void readFields (TrackCloudType &c)
 Read the fields associated with the owner cloud. More...
 
template<class TrackCloudType >
static void writeFields (const TrackCloudType &c)
 Write the fields associated with the owner cloud. More...
 

Friends

class Cloud< molecule >
 
Ostreamoperator<< (Ostream &, const molecule &)
 

Additional Inherited Members

- Static Public Attributes inherited from particle< Type >
static string propertyList_ = Foam::particle::propertyList()
 String representation of properties. More...
 
static label particleCount_ = 0
 Cumulative particle counter - used to provide unique ID. More...
 
- Protected Member Functions inherited from particle< Type >
template<class TrackCloudType >
bool hitPatch (TrackCloudType &, trackingData &)
 Overridable function to handle the particle hitting a patch. More...
 
template<class TrackCloudType >
void hitWedgePatch (TrackCloudType &, trackingData &)
 Overridable function to handle the particle hitting a wedgePatch. More...
 
template<class TrackCloudType >
void hitSymmetryPlanePatch (TrackCloudType &, trackingData &)
 Overridable function to handle the particle hitting a. More...
 
template<class TrackCloudType >
void hitSymmetryPatch (TrackCloudType &, trackingData &)
 Overridable function to handle the particle hitting a symmetryPatch. More...
 
template<class TrackCloudType >
void hitCyclicPatch (TrackCloudType &, trackingData &)
 Overridable function to handle the particle hitting a cyclicPatch. More...
 
template<class TrackCloudType >
void hitCyclicAMIPatch (const vector &displacement, const scalar fraction, TrackCloudType &cloud, trackingData &td)
 Overridable function to handle the particle hitting a cyclicAMIPatch. More...
 
template<class TrackCloudType >
void hitCyclicACMIPatch (const vector &displacement, const scalar fraction, TrackCloudType &cloud, trackingData &td)
 Overridable function to handle the particle hitting a. More...
 
template<class TrackCloudType >
void hitCyclicRepeatAMIPatch (const vector &displacement, const scalar fraction, TrackCloudType &cloud, trackingData &td)
 Overridable function to handle the particle hitting an. More...
 
template<class TrackCloudType >
void hitProcessorPatch (TrackCloudType &, trackingData &)
 Overridable function to handle the particle hitting a processorPatch. More...
 
template<class TrackCloudType >
void hitWallPatch (TrackCloudType &, trackingData &)
 Overridable function to handle the particle hitting a wallPatch. More...
 

Detailed Description

Foam::molecule.

Source files

Definition at line 64 of file molecule.H.

Member Enumeration Documentation

◆ specialTypes

Enumerator
SPECIAL_TETHERED 
SPECIAL_FROZEN 
NOT_SPECIAL 
SPECIAL_USER 

Definition at line 80 of file molecule.H.

Constructor & Destructor Documentation

◆ molecule() [1/3]

molecule ( const polyMesh mesh,
const barycentric coordinates,
const label  celli,
const label  tetFacei,
const label  tetPti,
const tensor Q,
const vector v,
const vector a,
const vector pi,
const vector tau,
const vector specialPosition,
const constantProperties constProps,
const label  special,
const label  id 
)
inline

Construct from components.

Definition at line 221 of file moleculeI.H.

References molecule::setSitePositions().

Referenced by molecule::clone(), molecule::constantProperties::constantProperties(), and molecule::iNew::operator()().

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◆ molecule() [2/3]

molecule ( const polyMesh mesh,
const vector position,
const label  celli,
const tensor Q,
const vector v,
const vector a,
const vector pi,
const vector tau,
const vector specialPosition,
const constantProperties constProps,
const label  special,
const label  id 
)
inline

Construct from a position and a cell, searching for the rest of the.

required topology

Definition at line 258 of file moleculeI.H.

References Foam::abort(), Foam::FatalError, FatalErrorInFunction, Foam::findIndex(), forAll, molecule::id(), Foam::mag(), Foam::nl, molecule::setSitePositions(), List< T >::setSize(), molecule::constantProperties::siteIds(), and List< T >::size().

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◆ molecule() [3/3]

molecule ( const polyMesh mesh,
Istream is,
bool  readFields = true 
)

Construct from Istream.

Definition at line 41 of file moleculeIO.C.

References IOstream::check(), IOstream::format(), Istream::read(), Foam::readLabel(), and readScalar.

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Member Function Documentation

◆ clone()

autoPtr<particle> clone ( ) const
inlinevirtual

Construct and return a clone.

Reimplemented from particle< Type >.

Definition at line 306 of file molecule.H.

References molecule::molecule().

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◆ move()

◆ transformProperties()

void transformProperties ( const transformer )
virtual

Transform the physical properties of the particle.

according to the given transformation tensor

Reimplemented from particle< Type >.

Definition at line 189 of file molecule.C.

References molecule::SPECIAL_TETHERED, transformer::T(), Tensor< Cmpt >::T(), transformer::transform(), transformer::transformList(), transformer::transformPosition(), and particle< Type >::transformProperties().

Referenced by molecule::iNew::operator()().

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◆ setSitePositions()

void setSitePositions ( const constantProperties constProps)

Definition at line 216 of file molecule.C.

References particle< Type >::position(), and molecule::constantProperties::siteReferencePositions().

Referenced by molecule::molecule(), molecule::move(), and molecule::iNew::operator()().

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◆ setSiteSizes()

void setSiteSizes ( label  size)

Definition at line 222 of file molecule.C.

References List< T >::setSize().

Referenced by molecule::iNew::operator()().

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◆ Q() [1/2]

const Foam::tensor & Q ( ) const
inline

Definition at line 501 of file moleculeI.H.

Referenced by molecule::constantProperties::constantProperties(), molecule::iNew::operator()(), molecule::readFields(), and molecule::writeFields().

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◆ Q() [2/2]

Foam::tensor & Q ( )
inline

Definition at line 507 of file moleculeI.H.

◆ v() [1/2]

const Foam::vector & v ( ) const
inline

Definition at line 513 of file moleculeI.H.

Referenced by molecule::iNew::operator()(), molecule::readFields(), and molecule::writeFields().

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◆ v() [2/2]

Foam::vector & v ( )
inline

Definition at line 519 of file moleculeI.H.

◆ a() [1/2]

const Foam::vector & a ( ) const
inline

Definition at line 525 of file moleculeI.H.

Referenced by molecule::iNew::operator()(), molecule::readFields(), and molecule::writeFields().

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◆ a() [2/2]

Foam::vector & a ( )
inline

Definition at line 531 of file moleculeI.H.

◆ pi() [1/2]

const Foam::vector & pi ( ) const
inline

Definition at line 537 of file moleculeI.H.

Referenced by molecule::iNew::operator()(), molecule::readFields(), and molecule::writeFields().

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◆ pi() [2/2]

Foam::vector & pi ( )
inline

Definition at line 543 of file moleculeI.H.

◆ tau() [1/2]

const Foam::vector & tau ( ) const
inline

Definition at line 549 of file moleculeI.H.

Referenced by molecule::iNew::operator()(), molecule::readFields(), and molecule::writeFields().

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◆ tau() [2/2]

Foam::vector & tau ( )
inline

Definition at line 555 of file moleculeI.H.

◆ siteForces() [1/2]

const Foam::List< Foam::vector > & siteForces ( ) const
inline

Definition at line 561 of file moleculeI.H.

Referenced by molecule::iNew::operator()().

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◆ siteForces() [2/2]

Foam::List< Foam::vector > & siteForces ( )
inline

Definition at line 567 of file moleculeI.H.

◆ sitePositions() [1/2]

const Foam::List< Foam::vector > & sitePositions ( ) const
inline

Definition at line 573 of file moleculeI.H.

Referenced by molecule::iNew::operator()().

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◆ sitePositions() [2/2]

Foam::List< Foam::vector > & sitePositions ( )
inline

Definition at line 579 of file moleculeI.H.

◆ specialPosition() [1/2]

const Foam::vector & specialPosition ( ) const
inline

Definition at line 585 of file moleculeI.H.

Referenced by molecule::iNew::operator()(), molecule::readFields(), and molecule::writeFields().

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◆ specialPosition() [2/2]

Foam::vector & specialPosition ( )
inline

Definition at line 591 of file moleculeI.H.

◆ potentialEnergy() [1/2]

Foam::scalar potentialEnergy ( ) const
inline

Definition at line 597 of file moleculeI.H.

Referenced by molecule::iNew::operator()().

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◆ potentialEnergy() [2/2]

Foam::scalar & potentialEnergy ( )
inline

Definition at line 603 of file moleculeI.H.

◆ rf() [1/2]

const Foam::tensor & rf ( ) const
inline

Definition at line 609 of file moleculeI.H.

Referenced by molecule::iNew::operator()().

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◆ rf() [2/2]

Foam::tensor & rf ( )
inline

Definition at line 615 of file moleculeI.H.

◆ special()

Foam::label special ( ) const
inline

Definition at line 621 of file moleculeI.H.

Referenced by molecule::iNew::operator()(), molecule::readFields(), and molecule::writeFields().

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◆ tethered()

bool tethered ( ) const
inline

Definition at line 627 of file moleculeI.H.

References molecule::SPECIAL_TETHERED.

Referenced by molecule::iNew::operator()().

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◆ id()

Foam::label id ( ) const
inline

Definition at line 633 of file moleculeI.H.

Referenced by molecule::molecule(), molecule::iNew::operator()(), molecule::readFields(), and molecule::writeFields().

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◆ hitPatch()

bool hitPatch ( moleculeCloud cloud,
trackingData td 
)

Overridable function to handle the particle hitting a patch.

Executed before other patch-hitting functions

Definition at line 230 of file molecule.C.

Referenced by molecule::iNew::operator()().

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◆ hitProcessorPatch()

void hitProcessorPatch ( moleculeCloud cloud,
trackingData td 
)

Overridable function to handle the particle hitting a processorPatch.

Definition at line 236 of file molecule.C.

References particle< Type >::trackingData::switchProcessor.

Referenced by molecule::iNew::operator()().

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◆ hitWallPatch()

void hitWallPatch ( moleculeCloud cloud,
trackingData td 
)

Overridable function to handle the particle hitting a wallPatch.

Definition at line 242 of file molecule.C.

References particle< Type >::normal(), and nw.

Referenced by molecule::iNew::operator()().

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◆ readFields()

◆ writeFields()

Friends And Related Function Documentation

◆ Cloud< molecule >

friend class Cloud< molecule >
friend

Definition at line 256 of file molecule.H.

◆ operator<<

Ostream& operator<< ( Ostream ,
const molecule  
)
friend

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